6-76674958-A-C

Variant names:

• chr6-76674958-A-C
• rs6919990

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 0.118 in 152,120 control chromosomes in the GnomAD database, including 1,155 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 0.12 (1155 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17897 AN: 152002 Hom.: 1152 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0469

Gnomad EAS AF: 0.0149

Gnomad SAS AF: 0.0990

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.118 AC: 17911 AN: 152120 Hom.: 1155 Cov.: 32 AF XY: 0.118 AC XY: 8775 AN XY: 74374

African (AFR) AF: 0.141 AC: 5849 AN: 41490

American (AMR) AF: 0.126 AC: 1920 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0469 AC: 163 AN: 3472

East Asian (EAS) AF: 0.0143 AC: 74 AN: 5162

South Asian (SAS) AF: 0.0988 AC: 477 AN: 4826

European-Finnish (FIN) AF: 0.146 AC: 1548 AN: 10580

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.112 AC: 7604 AN: 67998

Other (OTH) AF: 0.107 AC: 226 AN: 2112

Alfa AF: 0.111 Hom.: 527

Bravo AF: 0.116

Asia WGS AF: 0.0710 AC: 247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.69
DANN	Benign	0.35
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs6919990; hg19: chr6-77384675;