6-159140820-A-G

Variant names:

• chr6-159140820-A-G
• rs923459

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 0.484 in 152,138 control chromosomes in the GnomAD database, including 18,052 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 0.48 (18052 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.580

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 = 0.579 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: 0.484 AC: 73611 AN: 152020 Hom.: 18026 Cov.: 33

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.484 AC: 73684 AN: 152138 Hom.: 18052 Cov.: 33 AF XY: 0.486 AC XY: 36160 AN XY: 74370

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.596

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.484

Alfa AF: 0.493 Hom.: 3202

Bravo AF: 0.490

Asia WGS AF: 0.575 AC: 1996 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	2.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs923459; hg19: chr6-159561852; COSMIC: COSV69431681;