rs3131300

Variant names:

• chr6-32184157-A-G
• rs3131300
• ENST00000484849.5:n.90T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-32184157-A-G
• chr6-32184157-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000484849.5(AGER):​n.90T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 1,609,916 control chromosomes in the GnomAD database, including 25,894 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.14 (1733 hom., cov: 32)
  • Exomes 𝑓: 0.18 (24161 hom.)
• Consequence: AGER ENST00000484849.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.826
• Publications: 27 publications found

Genes affected

AGER (HGNC:320): (advanced glycosylation end-product specific receptor) The advanced glycosylation end product (AGE) receptor encoded by this gene is a member of the immunoglobulin superfamily of cell surface receptors. It is a multiligand receptor, and besides AGE, interacts with other molecules implicated in homeostasis, development, and inflammation, and certain diseases, such as diabetes and Alzheimer's disease. Many alternatively spliced transcript variants encoding different isoforms, as well as non-protein-coding variants, have been described for this gene (PMID:18089847). [provided by RefSeq, May 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGER	NM_001136.5	c.52+14T>C		intron_variant	Intron 1 of 10	ENST00000375076.9	NP_001127.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AGER	ENST00000375076.9	c.52+14T>C		intron_variant	Intron 1 of 10	1	NM_001136.5	ENSP00000364217.4

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21837 AN: 151970 Hom.: 1738 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.0817

Gnomad ASJ AF: 0.0875

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.128

GnomAD2 exomes AF: 0.135 AC: 32805 AN: 242884 AF XY: 0.137

Gnomad AFR exome AF: 0.123

Gnomad AMR exome AF: 0.0734

Gnomad ASJ exome AF: 0.0906

Gnomad EAS exome AF: 0.0907

Gnomad FIN exome AF: 0.132

Gnomad NFE exome AF: 0.170

Gnomad OTH exome AF: 0.132

GnomAD4 exome AF: 0.175 AC: 255563 AN: 1457828 Hom.: 24161 Cov.: 56 AF XY: 0.173 AC XY: 125573 AN XY: 725120

African (AFR) AF: 0.122 AC: 4069 AN: 33464

American (AMR) AF: 0.0773 AC: 3443 AN: 44528

Ashkenazi Jewish (ASJ) AF: 0.0934 AC: 2407 AN: 25784

East Asian (EAS) AF: 0.0972 AC: 3859 AN: 39686

South Asian (SAS) AF: 0.130 AC: 11195 AN: 85902

European-Finnish (FIN) AF: 0.136 AC: 7108 AN: 52118

Middle Eastern (MID) AF: 0.0672 AC: 385 AN: 5730

European-Non Finnish (NFE) AF: 0.192 AC: 212846 AN: 1110336

Other (OTH) AF: 0.170 AC: 10251 AN: 60280

GnomAD4 genome AF: 0.144 AC: 21827 AN: 152088 Hom.: 1733 Cov.: 32 AF XY: 0.139 AC XY: 10339 AN XY: 74344

African (AFR) AF: 0.116 AC: 4804 AN: 41498

American (AMR) AF: 0.0813 AC: 1244 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0875 AC: 303 AN: 3464

East Asian (EAS) AF: 0.105 AC: 542 AN: 5166

South Asian (SAS) AF: 0.154 AC: 744 AN: 4824

European-Finnish (FIN) AF: 0.138 AC: 1458 AN: 10598

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12227 AN: 67934

Other (OTH) AF: 0.127 AC: 269 AN: 2110

Alfa AF: 0.160 Hom.: 1491

Bravo AF: 0.140

Asia WGS AF: 0.114 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.1
DANN	Benign	0.61
PhyloP100		0.83
PromoterAI		0.014	Neutral
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3131300; hg19: chr6-32151934;