8-57378616-A-G

Variant names:

• chr8-57378616-A-G
• rs1317836

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 0.41 in 152,046 control chromosomes in the GnomAD database, including 16,005 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 0.41 (16005 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 0 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 = 0.732 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: 0.410 AC: 62281 AN: 151930 Hom.: 15977 Cov.: 32

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.410 AC: 62342 AN: 152046 Hom.: 16005 Cov.: 32 AF XY: 0.409 AC XY: 30426 AN XY: 74320

African (AFR) AF: 0.739 AC: 30659 AN: 41486

American (AMR) AF: 0.276 AC: 4213 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1190 AN: 3468

East Asian (EAS) AF: 0.334 AC: 1725 AN: 5166

South Asian (SAS) AF: 0.276 AC: 1327 AN: 4802

European-Finnish (FIN) AF: 0.330 AC: 3487 AN: 10580

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18655 AN: 67952

Other (OTH) AF: 0.381 AC: 804 AN: 2110

Alfa AF: 0.353 Hom.: 2241

Bravo AF: 0.416

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.26
DANN	Benign	0.37
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1317836; hg19: chr8-58291175; COSMIC: COSV70887938;