rs7096364

Variant names:

• chr10-111956344-A-G
• rs7096364
• ENST00000656217.1:n.132+16733T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000656217.1(ENSG00000287231):​n.132+16733T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,224 control chromosomes in the GnomAD database, including 1,980 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 0.13 (1980 hom., cov: 32)
• Consequence: ENSG00000287231 ENST00000656217.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.67

Genes affected

ENSG00000287231 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.425 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
ENSG00000287231	ENST00000656217.1	n.132+16733T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19625 AN: 152106 Hom.: 1981 Cov.: 32

Gnomad AFR AF: 0.0812

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.0856

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.0908

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.129 AC: 19636 AN: 152224 Hom.: 1980 Cov.: 32 AF XY: 0.136 AC XY: 10146 AN XY: 74430

Gnomad4 AFR AF: 0.0811

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.0856

Gnomad4 NFE AF: 0.0908

Gnomad4 OTH AF: 0.167

Alfa AF: 0.135 Hom.: 366

Bravo AF: 0.142

Asia WGS AF: 0.385 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.010
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7096364; hg19: chr10-113716102;