rs4646249

chr8-18402921-T-G

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 0.689 in 151,968 control chromosomes in the GnomAD database, including 36,849 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 0.69 (36849 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

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 (AFR) allele frequency at 95% confidence interval = 0.728 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: 0.690 AC: 104733 AN: 151850 Hom.: 36839 Cov.: 31

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.689 AC: 104781 AN: 151968 Hom.: 36849 Cov.: 31 AF XY: 0.683 AC XY: 50712 AN XY: 74276

Gnomad4 AFR AF: 0.735

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.800

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.687

Alfa AF: 0.712 Hom.: 49736

Bravo AF: 0.677

Asia WGS AF: 0.520 AC: 1811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.3
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4646249; hg19: chr8-18260431;