chr7-17359359-T-A

Variant names:

• chr7-17359359-T-A
• rs10269143
• ENST00000637807.1:c.2373+19131T>A

Variant summary

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

The ENST00000637807.1(ENSG00000283321):​c.2373+19131T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 151,968 control chromosomes in the GnomAD database, including 7,101 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 0.27 (7101 hom., cov: 32)
• Consequence: ENSG00000283321 ENST00000637807.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

Genes affected

ENSG00000283321 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.488 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
ENSG00000283321	ENST00000637807.1	c.2373+19131T>A		intron_variant	Intron 10 of 11	5		ENSP00000490530.1

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41264 AN: 151846 Hom.: 7068 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.272 AC: 41341 AN: 151968 Hom.: 7101 Cov.: 32 AF XY: 0.270 AC XY: 20065 AN XY: 74280

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.246

Alfa AF: 0.228 Hom.: 654

Bravo AF: 0.288

Asia WGS AF: 0.255 AC: 887 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	0.19
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10269143; hg19: chr7-17398983;