rs10249476

Variant names:

• chr7-128236973-G-T
• rs10249476
• ENST00000690022.2:n.51C>A

Variant summary

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

The ENST00000690022.2(ENSG00000289434):​n.51C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 151,972 control chromosomes in the GnomAD database, including 8,473 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 0.33 (8473 hom., cov: 32)
• Consequence: ENSG00000289434 ENST00000690022.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679
• Publications: 14 publications found

Genes affected

ENSG00000289434 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 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
ENSG00000289434	ENST00000690022.2	n.51C>A		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000289434	ENST00000692614.3	n.102C>A		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000289434	ENST00000785132.1	n.51C>A		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.329 AC: 50007 AN: 151854 Hom.: 8467 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.329 AC: 50047 AN: 151972 Hom.: 8473 Cov.: 32 AF XY: 0.327 AC XY: 24317 AN XY: 74290

African (AFR) AF: 0.265 AC: 10983 AN: 41430

American (AMR) AF: 0.365 AC: 5579 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1210 AN: 3468

East Asian (EAS) AF: 0.198 AC: 1023 AN: 5160

South Asian (SAS) AF: 0.293 AC: 1412 AN: 4814

European-Finnish (FIN) AF: 0.342 AC: 3611 AN: 10546

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25142 AN: 67966

Other (OTH) AF: 0.332 AC: 701 AN: 2112

Alfa AF: 0.348 Hom.: 11219

Bravo AF: 0.333

Asia WGS AF: 0.230 AC: 800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.53
DANN	Benign	0.39
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs10249476; hg19: chr7-127877026;