chr6-170595870-C-T

Variant names:

• chr6-170595870-C-T
• rs2206285
• ENST00000833512.1:n.107-1108G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000833512.1(ENSG00000308355):​n.107-1108G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000308355 ENST00000833512.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 1 publications found

Genes affected

ENSG00000308355 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308355	ENST00000833512.1	n.107-1108G>A		intron_variant	Intron 1 of 3
ENSG00000308355	ENST00000833513.1	n.107-1108G>A		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.0882 AC: 3662 AN: 41526

American (AMR) AF: 0.0546 AC: 836 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0703 AC: 244 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.00559 AC: 27 AN: 4828

European-Finnish (FIN) AF: 0.0333 AC: 353 AN: 10612

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0551 AC: 3746 AN: 68020

Other (OTH) AF: 0.0558 AC: 118 AN: 2116

Alfa AF: 0.0600 Hom.: 38

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
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs2206285; hg19: chr6-170904958;