rs6902257

Variant names:

• chr6-80771637-G-A
• rs6902257

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 0.0324 in 152,176 control chromosomes in the GnomAD database, including 136 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 0.032 (136 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.129 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: 0.0325 AC: 4937 AN: 152060 Hom.: 136 Cov.: 31

Gnomad AFR AF: 0.0370

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0252

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0220

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0273

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0324 AC: 4937 AN: 152176 Hom.: 136 Cov.: 31 AF XY: 0.0343 AC XY: 2548 AN XY: 74392

African (AFR) AF: 0.0369 AC: 1534 AN: 41520

American (AMR) AF: 0.0251 AC: 384 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0170 AC: 59 AN: 3472

East Asian (EAS) AF: 0.0133 AC: 69 AN: 5182

South Asian (SAS) AF: 0.138 AC: 663 AN: 4816

European-Finnish (FIN) AF: 0.0220 AC: 233 AN: 10596

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0273 AC: 1855 AN: 67998

Other (OTH) AF: 0.0336 AC: 71 AN: 2114

Alfa AF: 0.0281 Hom.: 136

Bravo AF: 0.0307

Asia WGS AF: 0.0820 AC: 289 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.74
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs6902257; hg19: chr6-81481354;