chr6-19051464-C-T

Variant names:

• chr6-19051464-C-T
• rs926274
• ENST00000772974.1:n.620+34697G>A

Variant summary

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

The ENST00000772974.1(ENSG00000300612):​n.620+34697G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,878 control chromosomes in the GnomAD database, including 24,798 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 0.57 (24798 hom., cov: 31)
• Consequence: ENSG00000300612 ENST00000772974.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 7 publications found

Genes affected

ENSG00000300612 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374958	XR_001744010.1	n.398+25677C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300612	ENST00000772974.1	n.620+34697G>A		intron_variant	Intron 4 of 4
ENSG00000300612	ENST00000772975.1	n.363+34697G>A		intron_variant	Intron 3 of 3
ENSG00000300612	ENST00000772976.1	n.339+34697G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86401 AN: 151760 Hom.: 24797 Cov.: 31

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.569 AC: 86433 AN: 151878 Hom.: 24798 Cov.: 31 AF XY: 0.571 AC XY: 42417 AN XY: 74252

African (AFR) AF: 0.525 AC: 21741 AN: 41412

American (AMR) AF: 0.511 AC: 7793 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1875 AN: 3466

East Asian (EAS) AF: 0.564 AC: 2906 AN: 5150

South Asian (SAS) AF: 0.615 AC: 2952 AN: 4802

European-Finnish (FIN) AF: 0.671 AC: 7092 AN: 10576

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40178 AN: 67910

Other (OTH) AF: 0.589 AC: 1237 AN: 2100

Alfa AF: 0.579 Hom.: 109214

Bravo AF: 0.552

Asia WGS AF: 0.579 AC: 2014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.2
DANN	Benign	0.71
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs926274; hg19: chr6-19051695;