6-19051464-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772974.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300612	ENST00000772974.1		n.620+34697G>A		intron	N/A
	ENSG00000300612	ENST00000772975.1		n.363+34697G>A		intron	N/A
	ENSG00000300612	ENST00000772976.1		n.339+34697G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs926274;

hg19: chr6-19051695;