6-92112837-G-A

Variant names:

• chr6-92112837-G-A
• rs2452941
• ENST00000647772.1:n.32+67288C>T

Variant summary

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

The ENST00000647772.1(ENSG00000285961):​n.32+67288C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 152,032 control chromosomes in the GnomAD database, including 18,806 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 0.49 (18806 hom., cov: 33)
• Consequence: ENSG00000285961 ENST00000647772.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567
• Publications: 3 publications found

Genes affected

ENSG00000285961 (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 = 0.673 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
ENSG00000285961	ENST00000647772.1	n.32+67288C>T		intron_variant	Intron 1 of 4
ENSG00000285961	ENST00000742295.1	n.126+10924C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74134 AN: 151914 Hom.: 18790 Cov.: 33

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.488 AC: 74174 AN: 152032 Hom.: 18806 Cov.: 33 AF XY: 0.491 AC XY: 36525 AN XY: 74336

African (AFR) AF: 0.339 AC: 14054 AN: 41476

American (AMR) AF: 0.570 AC: 8700 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1887 AN: 3468

East Asian (EAS) AF: 0.691 AC: 3579 AN: 5176

South Asian (SAS) AF: 0.595 AC: 2870 AN: 4822

European-Finnish (FIN) AF: 0.530 AC: 5597 AN: 10560

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35615 AN: 67950

Other (OTH) AF: 0.535 AC: 1124 AN: 2102

Alfa AF: 0.500 Hom.: 3439

Bravo AF: 0.486

Asia WGS AF: 0.639 AC: 2222 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.29
DANN	Benign	0.22
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs2452941; hg19: chr6-92822555; COSMIC: COSV60246485;