6-160335005-C-T

Position:

• chr6-160335005-C-T

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 0.639 in 151,860 control chromosomes in the GnomAD database, including 31,274 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 0.64 (31274 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.668 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: 0.639 AC: 96939 AN: 151742 Hom.: 31237 Cov.: 31

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.639 AC: 97020 AN: 151860 Hom.: 31274 Cov.: 31 AF XY: 0.633 AC XY: 46944 AN XY: 74194

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.628

Alfa AF: 0.663 Hom.: 33465

Bravo AF: 0.634

Asia WGS AF: 0.452 AC: 1574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.47
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs316170; hg19: chr6-160756037;