6-127957653-A-G

Variant names:

• chr6-127957653-A-G
• rs802734

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 0.233 in 152,112 control chromosomes in the GnomAD database, including 4,713 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 0.23 (4713 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276
• Publications: 57 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 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: 0.233 AC: 35459 AN: 151994 Hom.: 4716 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.233 AC: 35465 AN: 152112 Hom.: 4713 Cov.: 32 AF XY: 0.232 AC XY: 17246 AN XY: 74352

African (AFR) AF: 0.131 AC: 5456 AN: 41524

American (AMR) AF: 0.225 AC: 3438 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 786 AN: 3464

East Asian (EAS) AF: 0.138 AC: 711 AN: 5162

South Asian (SAS) AF: 0.261 AC: 1258 AN: 4816

European-Finnish (FIN) AF: 0.267 AC: 2827 AN: 10580

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20135 AN: 67960

Other (OTH) AF: 0.257 AC: 542 AN: 2112

Alfa AF: 0.274 Hom.: 23528

Bravo AF: 0.229

Asia WGS AF: 0.211 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.60
DANN	Benign	0.31
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs802734; hg19: chr6-128278798;