rs10945617

Variant names:

• chr6-159531400-G-A
• rs10945617
• ENST00000656085.1:n.43-61885C>T

Variant summary

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

The ENST00000656085.1(ENSG00000286533):​n.43-61885C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,134 control chromosomes in the GnomAD database, including 3,718 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 0.22 (3718 hom., cov: 32)
• Consequence: ENSG00000286533 ENST00000656085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 4 publications found

Genes affected

ENSG00000286533 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 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
ENSG00000286533	ENST00000656085.1	n.43-61885C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32827 AN: 152016 Hom.: 3714 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.216 AC: 32853 AN: 152134 Hom.: 3718 Cov.: 32 AF XY: 0.213 AC XY: 15811 AN XY: 74362

African (AFR) AF: 0.276 AC: 11471 AN: 41488

American (AMR) AF: 0.145 AC: 2218 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 529 AN: 3468

East Asian (EAS) AF: 0.215 AC: 1107 AN: 5152

South Asian (SAS) AF: 0.207 AC: 996 AN: 4818

European-Finnish (FIN) AF: 0.201 AC: 2130 AN: 10586

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13787 AN: 68002

Other (OTH) AF: 0.188 AC: 398 AN: 2116

Alfa AF: 0.200 Hom.: 13297

Bravo AF: 0.211

Asia WGS AF: 0.200 AC: 696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.62
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs10945617; hg19: chr6-159952432;