ENST00000656775.1:n.689+3656A>G

Variant names:

• chr10-4035359-A-G
• rs2645227
• ENST00000656775.1:n.689+3656A>G

Variant summary

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

The ENST00000656775.1(ENSG00000227101):​n.689+3656A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,100 control chromosomes in the GnomAD database, including 6,793 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 0.25 (6793 hom., cov: 32)
• Consequence: ENSG00000227101 ENST00000656775.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 0 publications found

Genes affected

ENSG00000227101 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984195	NR_176060.1	n.613+3656A>G		intron_variant	Intron 2 of 9
LOC107984195	NR_176062.1	n.613+3656A>G		intron_variant	Intron 2 of 3
LOC107984195	NR_176063.1	n.867+3656A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227101	ENST00000656775.1	n.689+3656A>G		intron_variant	Intron 2 of 2
ENSG00000227101	ENST00000658139.1	n.568+3656A>G		intron_variant	Intron 2 of 2
ENSG00000227101	ENST00000667089.1	n.627+3656A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38413 AN: 151980 Hom.: 6769 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0734

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.253 AC: 38498 AN: 152100 Hom.: 6793 Cov.: 32 AF XY: 0.244 AC XY: 18143 AN XY: 74378

African (AFR) AF: 0.501 AC: 20763 AN: 41442

American (AMR) AF: 0.175 AC: 2673 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 828 AN: 3468

East Asian (EAS) AF: 0.249 AC: 1285 AN: 5168

South Asian (SAS) AF: 0.182 AC: 880 AN: 4824

European-Finnish (FIN) AF: 0.0734 AC: 779 AN: 10608

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10427 AN: 67986

Other (OTH) AF: 0.247 AC: 521 AN: 2106

Alfa AF: 0.216 Hom.: 621

Bravo AF: 0.273

Asia WGS AF: 0.229 AC: 795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.23
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs2645227; hg19: chr10-4077551;