rs1496112

Variant names:

• chr6-140223977-G-T
• rs1496112
• ENST00000683950.1:n.201+75287G>T

Variant summary

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

The ENST00000683950.1(ENSG00000288714):​n.201+75287G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,114 control chromosomes in the GnomAD database, including 2,831 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 0.18 (2831 hom., cov: 32)
• Consequence: ENSG00000288714 ENST00000683950.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.702
• Publications: 2 publications found

Genes affected

ENSG00000288714 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288714	ENST00000683950.1	n.201+75287G>T		intron_variant	Intron 1 of 1
ENSG00000288714	ENST00000825769.1	n.175+75287G>T		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27299 AN: 151994 Hom.: 2831 Cov.: 32

Gnomad AFR AF: 0.0882

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.177

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.180 AC: 27313 AN: 152114 Hom.: 2831 Cov.: 32 AF XY: 0.180 AC XY: 13384 AN XY: 74338

African (AFR) AF: 0.0883 AC: 3668 AN: 41548

American (AMR) AF: 0.205 AC: 3135 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 849 AN: 3466

East Asian (EAS) AF: 0.409 AC: 2112 AN: 5162

South Asian (SAS) AF: 0.183 AC: 885 AN: 4824

European-Finnish (FIN) AF: 0.219 AC: 2317 AN: 10564

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13783 AN: 67960

Other (OTH) AF: 0.179 AC: 379 AN: 2116

Alfa AF: 0.183 Hom.: 487

Bravo AF: 0.176

Asia WGS AF: 0.284 AC: 982 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.32
DANN	Benign	0.23
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs1496112; hg19: chr6-140545114;