8-5213890-T-C

Variant names:

• chr8-5213890-T-C
• rs7816936

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 0.515 in 151,878 control chromosomes in the GnomAD database, including 20,957 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 0.52 (20957 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

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 (NFE) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78219 AN: 151758 Hom.: 20956 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.515 AC: 78248 AN: 151878 Hom.: 20957 Cov.: 32 AF XY: 0.506 AC XY: 37595 AN XY: 74246

African (AFR) AF: 0.509 AC: 21050 AN: 41384

American (AMR) AF: 0.491 AC: 7496 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2203 AN: 3464

East Asian (EAS) AF: 0.110 AC: 571 AN: 5168

South Asian (SAS) AF: 0.427 AC: 2059 AN: 4824

European-Finnish (FIN) AF: 0.438 AC: 4626 AN: 10552

Middle Eastern (MID) AF: 0.705 AC: 206 AN: 292

European-Non Finnish (NFE) AF: 0.564 AC: 38336 AN: 67918

Other (OTH) AF: 0.562 AC: 1184 AN: 2108

Alfa AF: 0.542 Hom.: 62865

Bravo AF: 0.516

Asia WGS AF: 0.308 AC: 1070 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.80
DANN	Benign	0.48
PhyloP100		-1.6

Splicing

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

Publications

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Other links and lift over

dbSNP: rs7816936; hg19: chr8-5071412;