rs957646

Variant names:

• chr10-90304565-T-C
• rs957646
• ENST00000749546.1:n.227+12471A>G

Variant summary

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

The ENST00000749546.1(ENSG00000297645):​n.227+12471A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0937 in 152,162 control chromosomes in the GnomAD database, including 1,212 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 0.094 (1212 hom., cov: 32)
• Consequence: ENSG00000297645 ENST00000749546.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370
• Publications: 1 publications found

Genes affected

ENSG00000297645 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000749546.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297645	ENST00000749546.1		n.227+12471A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0938 AC: 14256 AN: 152044 Hom.: 1212 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0603

Gnomad ASJ AF: 0.0562

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0213

Gnomad FIN AF: 0.0270

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0450

Gnomad OTH AF: 0.0752

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

GnomAD4 genome AF: 0.0937 AC: 14260 AN: 152162 Hom.: 1212 Cov.: 32 AF XY: 0.0903 AC XY: 6717 AN XY: 74404

African (AFR) AF: 0.229 AC: 9495 AN: 41476

American (AMR) AF: 0.0602 AC: 920 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0562 AC: 195 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.0211 AC: 102 AN: 4830

European-Finnish (FIN) AF: 0.0270 AC: 286 AN: 10610

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0450 AC: 3058 AN: 68004

Other (OTH) AF: 0.0744 AC: 157 AN: 2110

Alfa AF: 0.0656 Hom.: 106

Bravo AF: 0.103

Asia WGS AF: 0.0250 AC: 90 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.76
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs957646; hg19: chr10-92064322;