chr8-57313501-T-C

Position:

• chr8-57313501-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.291

Alfa AF: 0.203 Hom.: 5565

Bravo AF: 0.308

Asia WGS AF: 0.307 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7013994; hg19: chr8-58226060;