rs12462800

Variant names:

• chr19-35355974-G-A
• rs12462800
• ENST00000716259.1:n.771-8352C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-35355974-G-A
• chr19-35355974-G-C
• chr19-35355974-G-T

Variant summary

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

The ENST00000716259.1(ENSG00000288731):​n.771-8352C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,014 control chromosomes in the GnomAD database, including 1,103 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 0.11 (1103 hom., cov: 32)
• Consequence: ENSG00000288731 ENST00000716259.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.09
• Publications: 6 publications found

Genes affected

ENSG00000288731 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 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
ENSG00000288731	ENST00000716259.1	n.771-8352C>T		intron_variant	Intron 2 of 2
ENSG00000288731	ENST00000786314.1	n.648-8352C>T		intron_variant	Intron 2 of 2
ENSG00000288731	ENST00000786315.1	n.160-8352C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16166 AN: 151896 Hom.: 1104 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.0677

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0579

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.106 AC: 16177 AN: 152014 Hom.: 1103 Cov.: 32 AF XY: 0.111 AC XY: 8237 AN XY: 74300

African (AFR) AF: 0.137 AC: 5670 AN: 41444

American (AMR) AF: 0.178 AC: 2716 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0677 AC: 235 AN: 3472

East Asian (EAS) AF: 0.259 AC: 1340 AN: 5178

South Asian (SAS) AF: 0.176 AC: 849 AN: 4818

European-Finnish (FIN) AF: 0.104 AC: 1096 AN: 10566

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0579 AC: 3933 AN: 67954

Other (OTH) AF: 0.0946 AC: 199 AN: 2104

Alfa AF: 0.0700 Hom.: 881

Bravo AF: 0.113

Asia WGS AF: 0.199 AC: 690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.57
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs12462800; hg19: chr19-35846876;