6-163619491-C-G

Variant names:

• chr6-163619491-C-G
• rs6900149

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 0.676 in 151,872 control chromosomes in the GnomAD database, including 35,443 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 0.68 (35443 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480
• Publications: 3 publications found

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 (AFR) allele frequency at 95% confidence interval = 0.807 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: 0.676 AC: 102563 AN: 151754 Hom.: 35409 Cov.: 30

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.676 AC: 102639 AN: 151872 Hom.: 35443 Cov.: 30 AF XY: 0.666 AC XY: 49436 AN XY: 74198

African (AFR) AF: 0.815 AC: 33741 AN: 41416

American (AMR) AF: 0.596 AC: 9100 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2263 AN: 3470

East Asian (EAS) AF: 0.542 AC: 2781 AN: 5132

South Asian (SAS) AF: 0.575 AC: 2759 AN: 4800

European-Finnish (FIN) AF: 0.551 AC: 5810 AN: 10544

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44056 AN: 67940

Other (OTH) AF: 0.680 AC: 1432 AN: 2106

Alfa AF: 0.670 Hom.: 4330

Bravo AF: 0.690

Asia WGS AF: 0.563 AC: 1959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.0
DANN	Benign	0.46
PhyloP100		0.048

Splicing

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

Other links and lift over

dbSNP: rs6900149; hg19: chr6-164040523; COSMIC: COSV69432300;