chr6-67471804-T-C

Variant names:

• chr6-67471804-T-C
• rs4710654

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 0.441 in 151,798 control chromosomes in the GnomAD database, including 15,241 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 0.44 (15241 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66849 AN: 151680 Hom.: 15233 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.441 AC: 66897 AN: 151798 Hom.: 15241 Cov.: 32 AF XY: 0.436 AC XY: 32366 AN XY: 74174

African (AFR) AF: 0.557 AC: 23057 AN: 41386

American (AMR) AF: 0.437 AC: 6643 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1559 AN: 3466

East Asian (EAS) AF: 0.197 AC: 1014 AN: 5160

South Asian (SAS) AF: 0.382 AC: 1842 AN: 4820

European-Finnish (FIN) AF: 0.376 AC: 3969 AN: 10564

Middle Eastern (MID) AF: 0.500 AC: 145 AN: 290

European-Non Finnish (NFE) AF: 0.402 AC: 27269 AN: 67890

Other (OTH) AF: 0.439 AC: 926 AN: 2110

Alfa AF: 0.432 Hom.: 1904

Bravo AF: 0.448

Asia WGS AF: 0.306 AC: 1068 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.81
DANN	Benign	0.53
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs4710654; hg19: chr6-68181697;