6-170595870-C-T

Position:

• chr6-170595870-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 0.0592 in 152,266 control chromosomes in the GnomAD database, including 325 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 0.059 (325 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0858 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: 0.0593 AC: 9019 AN: 152148 Hom.: 325 Cov.: 33

Gnomad AFR AF: 0.0883

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0548

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.00559

Gnomad FIN AF: 0.0333

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0551

Gnomad OTH AF: 0.0564

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

GnomAD4 genome AF: 0.0592 AC: 9021 AN: 152266 Hom.: 325 Cov.: 33 AF XY: 0.0570 AC XY: 4247 AN XY: 74476

Gnomad4 AFR AF: 0.0882

Gnomad4 AMR AF: 0.0546

Gnomad4 ASJ AF: 0.0703

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.00559

Gnomad4 FIN AF: 0.0333

Gnomad4 NFE AF: 0.0551

Gnomad4 OTH AF: 0.0558

Alfa AF: 0.0588 Hom.: 36

Bravo AF: 0.0615

Asia WGS AF: 0.0100 AC: 35 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
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: rs2206285; hg19: chr6-170904958;