6-67471879-T-C

Variant names:

• chr6-67471879-T-C
• rs4710655

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 0.453 in 151,990 control chromosomes in the GnomAD database, including 16,357 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 0.45 (16357 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 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: 0.453 AC: 68756 AN: 151872 Hom.: 16346 Cov.: 33

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.453 AC: 68809 AN: 151990 Hom.: 16357 Cov.: 33 AF XY: 0.448 AC XY: 33279 AN XY: 74286

African (AFR) AF: 0.599 AC: 24849 AN: 41476

American (AMR) AF: 0.441 AC: 6709 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1563 AN: 3470

East Asian (EAS) AF: 0.196 AC: 1013 AN: 5166

South Asian (SAS) AF: 0.382 AC: 1845 AN: 4824

European-Finnish (FIN) AF: 0.376 AC: 3970 AN: 10566

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27302 AN: 67948

Other (OTH) AF: 0.446 AC: 938 AN: 2104

Alfa AF: 0.439 Hom.: 2475

Bravo AF: 0.462

Asia WGS AF: 0.309 AC: 1078 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.50
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs4710655; hg19: chr6-68181772; COSMIC: COSV72736802;