chr8-57313501-T-C

Variant names:

• chr8-57313501-T-C
• rs7013994

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 0.297 in 152,050 control chromosomes in the GnomAD database, including 8,415 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 0.30 (8415 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.05
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 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: 0.297 AC: 45150 AN: 151932 Hom.: 8392 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.297 AC: 45224 AN: 152050 Hom.: 8415 Cov.: 32 AF XY: 0.296 AC XY: 21966 AN XY: 74330

African (AFR) AF: 0.535 AC: 22184 AN: 41438

American (AMR) AF: 0.223 AC: 3403 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 646 AN: 3472

East Asian (EAS) AF: 0.306 AC: 1575 AN: 5154

South Asian (SAS) AF: 0.200 AC: 964 AN: 4822

European-Finnish (FIN) AF: 0.205 AC: 2167 AN: 10570

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.197 AC: 13415 AN: 68010

Other (OTH) AF: 0.291 AC: 615 AN: 2112

Alfa AF: 0.233 Hom.: 11958

Bravo AF: 0.308

Asia WGS AF: 0.307 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.037
DANN	Benign	0.58
PhyloP100		-5.0

Splicing

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

Other links and lift over

dbSNP: rs7013994; hg19: chr8-58226060;