rs13277254

chr8-42694839-G-A

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 0.664 in 152,144 control chromosomes in the GnomAD database, including 35,747 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 0.66 (35747 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

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 (EAS) allele frequency at 95% confidence interval = 0.786 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: 0.664 AC: 100921 AN: 152026 Hom.: 35731 Cov.: 33

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.664 AC: 100968 AN: 152144 Hom.: 35747 Cov.: 33 AF XY: 0.667 AC XY: 49636 AN XY: 74378

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.723

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.711

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.688

Alfa AF: 0.712 Hom.: 4958

Bravo AF: 0.649

Asia WGS AF: 0.713 AC: 2479 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	1.8
Dann	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13277254; hg19: chr8-42549982;