6-71543357-T-C

Variant names:

• chr6-71543357-T-C
• rs199630

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 0.622 in 151,902 control chromosomes in the GnomAD database, including 30,719 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 0.62 (30719 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 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: 0.622 AC: 94395 AN: 151784 Hom.: 30674 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.622 AC: 94498 AN: 151902 Hom.: 30719 Cov.: 31 AF XY: 0.623 AC XY: 46225 AN XY: 74220

African (AFR) AF: 0.820 AC: 33983 AN: 41462

American (AMR) AF: 0.598 AC: 9125 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1570 AN: 3460

East Asian (EAS) AF: 0.686 AC: 3546 AN: 5170

South Asian (SAS) AF: 0.633 AC: 3049 AN: 4818

European-Finnish (FIN) AF: 0.513 AC: 5396 AN: 10520

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35905 AN: 67902

Other (OTH) AF: 0.600 AC: 1270 AN: 2116

Alfa AF: 0.553 Hom.: 9138

Bravo AF: 0.637

Asia WGS AF: 0.694 AC: 2407 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.78
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs199630; hg19: chr6-72253060;