6-159302471-C-G

Position:

• chr6-159302471-C-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 0.535 in 152,056 control chromosomes in the GnomAD database, including 25,018 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 0.54 (25018 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.447

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81360 AN: 151938 Hom.: 25020 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.535 AC: 81362 AN: 152056 Hom.: 25018 Cov.: 32 AF XY: 0.536 AC XY: 39870 AN XY: 74346

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.588

Alfa AF: 0.592 Hom.: 3469

Bravo AF: 0.517

Asia WGS AF: 0.426 AC: 1483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.81
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4708818; hg19: chr6-159723503; COSMIC: COSV60298415;