chr4-6269344-T-C

Variant names:

• chr4-6269344-T-C
• rs13107806

Variant summary

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

The variant allele was found at a frequency of 0.569 in 152,172 control chromosomes in the GnomAD database, including 25,563 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 (25563 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.913 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

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86513 AN: 152054 Hom.: 25541 Cov.: 34

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.569 AC: 86576 AN: 152172 Hom.: 25563 Cov.: 34 AF XY: 0.574 AC XY: 42696 AN XY: 74392

African (AFR) AF: 0.463 AC: 19206 AN: 41504

American (AMR) AF: 0.655 AC: 10019 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2310 AN: 3472

East Asian (EAS) AF: 0.935 AC: 4846 AN: 5182

South Asian (SAS) AF: 0.668 AC: 3226 AN: 4828

European-Finnish (FIN) AF: 0.549 AC: 5809 AN: 10590

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39307 AN: 67990

Other (OTH) AF: 0.597 AC: 1261 AN: 2114

Alfa AF: 0.584 Hom.: 37996

Bravo AF: 0.573

Asia WGS AF: 0.770 AC: 2678 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.55
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs13107806; hg19: chr4-6271071;