chr6-13571363-T-G

Variant names:

• chr6-13571363-T-G
• rs2841505

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 0.3 in 151,890 control chromosomes in the GnomAD database, including 6,928 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 0.30 (6928 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.530
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.32 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: 0.299 AC: 45449 AN: 151772 Hom.: 6915 Cov.: 31

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.300 AC: 45504 AN: 151890 Hom.: 6928 Cov.: 31 AF XY: 0.301 AC XY: 22322 AN XY: 74248

African (AFR) AF: 0.291 AC: 12056 AN: 41378

American (AMR) AF: 0.328 AC: 4995 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 880 AN: 3470

East Asian (EAS) AF: 0.125 AC: 649 AN: 5180

South Asian (SAS) AF: 0.309 AC: 1491 AN: 4820

European-Finnish (FIN) AF: 0.329 AC: 3466 AN: 10550

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.311 AC: 21117 AN: 67926

Other (OTH) AF: 0.304 AC: 643 AN: 2114

Alfa AF: 0.279 Hom.: 2598

Bravo AF: 0.295

Asia WGS AF: 0.255 AC: 888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.8
DANN	Benign	0.63
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs2841505; hg19: chr6-13571595;