8-49628149-T-C

Position:

• chr8-49628149-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 0.861 in 151,950 control chromosomes in the GnomAD database, including 56,710 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 0.86 (56710 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.905 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: 0.861 AC: 130677 AN: 151836 Hom.: 56671 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.859

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.861 AC: 130773 AN: 151950 Hom.: 56710 Cov.: 32 AF XY: 0.863 AC XY: 64076 AN XY: 74286

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.849

Gnomad4 ASJ AF: 0.940

Gnomad4 EAS AF: 0.910

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.964

Gnomad4 NFE AF: 0.911

Gnomad4 OTH AF: 0.851

Alfa AF: 0.896 Hom.: 22154

Bravo AF: 0.847

Asia WGS AF: 0.847 AC: 2915 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1496306; hg19: chr8-50540708;