rs7913069

Variant names:

• chr10-103954641-C-T
• rs7913069
• ENST00000698239.1:n.273+5122G>A

Variant summary

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

The ENST00000698239.1(ENSG00000289744):​n.273+5122G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0693 in 152,116 control chromosomes in the GnomAD database, including 640 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 0.069 (640 hom., cov: 32)
• Consequence: ENSG00000289744 ENST00000698239.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 24 publications found

Genes affected

ENSG00000289744 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724351	XR_007062278.1	n.1343+5122G>A		intron_variant	Intron 2 of 2
LOC102724351	XR_007062279.1	n.481+3818G>A		intron_variant	Intron 3 of 3
LOC102724351	XR_007062282.1	n.1431+3818G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289744	ENST00000698239.1	n.273+5122G>A		intron_variant	Intron 2 of 11
ENSG00000289744	ENST00000698240.1	n.388+5122G>A		intron_variant	Intron 2 of 10
ENSG00000289745	ENST00000698306.2	n.372+5122G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0691 AC: 10506 AN: 151998 Hom.: 637 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.0959

Gnomad ASJ AF: 0.0161

Gnomad EAS AF: 0.0820

Gnomad SAS AF: 0.0705

Gnomad FIN AF: 0.0694

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0172

Gnomad OTH AF: 0.0675

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

GnomAD4 genome AF: 0.0693 AC: 10539 AN: 152116 Hom.: 640 Cov.: 32 AF XY: 0.0718 AC XY: 5341 AN XY: 74362

African (AFR) AF: 0.149 AC: 6160 AN: 41474

American (AMR) AF: 0.0963 AC: 1472 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0161 AC: 56 AN: 3470

East Asian (EAS) AF: 0.0827 AC: 429 AN: 5186

South Asian (SAS) AF: 0.0704 AC: 339 AN: 4818

European-Finnish (FIN) AF: 0.0694 AC: 733 AN: 10568

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0172 AC: 1173 AN: 68002

Other (OTH) AF: 0.0663 AC: 140 AN: 2112

Alfa AF: 0.0337 Hom.: 681

Bravo AF: 0.0753

Asia WGS AF: 0.0970 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.9
DANN	Benign	0.62
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs7913069; hg19: chr10-105714399;