6-31585073-T-C

Variant names:

• chr6-31585073-T-C
• rs7758790

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 0.224 in 151,538 control chromosomes in the GnomAD database, including 3,900 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 0.22 (3900 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.386 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: 0.224 AC: 33968 AN: 151424 Hom.: 3894 Cov.: 31

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.224 AC: 34012 AN: 151538 Hom.: 3900 Cov.: 31 AF XY: 0.225 AC XY: 16633 AN XY: 74032

African (AFR) AF: 0.211 AC: 8697 AN: 41250

American (AMR) AF: 0.206 AC: 3134 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 944 AN: 3466

East Asian (EAS) AF: 0.172 AC: 882 AN: 5118

South Asian (SAS) AF: 0.401 AC: 1927 AN: 4802

European-Finnish (FIN) AF: 0.182 AC: 1908 AN: 10510

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.231 AC: 15680 AN: 67856

Other (OTH) AF: 0.266 AC: 558 AN: 2098

Alfa AF: 0.219 Hom.: 485

Bravo AF: 0.224

Asia WGS AF: 0.290 AC: 1006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.64
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs7758790; hg19: chr6-31552850;