chr6-98563625-A-G

Position:

• chr6-98563625-A-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 0.824 in 152,088 control chromosomes in the GnomAD database, including 52,693 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 0.82 (52693 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.893 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: 0.825 AC: 125323 AN: 151970 Hom.: 52668 Cov.: 31

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.914

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.950

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.824 AC: 125392 AN: 152088 Hom.: 52693 Cov.: 31 AF XY: 0.827 AC XY: 61536 AN XY: 74364

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.822

Gnomad4 EAS AF: 0.915

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.950

Gnomad4 NFE AF: 0.890

Gnomad4 OTH AF: 0.832

Alfa AF: 0.876 Hom.: 79374

Bravo AF: 0.812

Asia WGS AF: 0.857 AC: 2982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.2
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2086512; hg19: chr6-99011501;