rs10239907

Variant names:

• chr7-25092760-G-A
• rs10239907
• ENST00000737690.1:n.51-17122G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-25092760-G-A
• chr7-25092760-G-C

Variant summary

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

The ENST00000737690.1(ENSG00000296268):​n.51-17122G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 151,570 control chromosomes in the GnomAD database, including 3,769 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 0.22 (3769 hom., cov: 31)
• Consequence: ENSG00000296268 ENST00000737690.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113
• Publications: 3 publications found

Genes affected

ENSG00000296268 (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 (EAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737690.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296268	ENST00000737690.1		n.51-17122G>A		intron	N/A
	ENSG00000296268	ENST00000737691.1		n.211+7647G>A		intron	N/A
	ENSG00000296268	ENST00000737692.1		n.52-17122G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33125 AN: 151466 Hom.: 3766 Cov.: 31

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.219 AC: 33141 AN: 151570 Hom.: 3769 Cov.: 31 AF XY: 0.222 AC XY: 16440 AN XY: 74044

African (AFR) AF: 0.157 AC: 6472 AN: 41350

American (AMR) AF: 0.268 AC: 4088 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 725 AN: 3468

East Asian (EAS) AF: 0.316 AC: 1630 AN: 5152

South Asian (SAS) AF: 0.250 AC: 1196 AN: 4792

European-Finnish (FIN) AF: 0.250 AC: 2594 AN: 10366

Middle Eastern (MID) AF: 0.286 AC: 83 AN: 290

European-Non Finnish (NFE) AF: 0.232 AC: 15739 AN: 67896

Other (OTH) AF: 0.213 AC: 448 AN: 2106

Alfa AF: 0.227 Hom.: 15558

Bravo AF: 0.214

Asia WGS AF: 0.228 AC: 794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.2
DANN	Benign	0.76
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10239907; hg19: chr7-25132379; COSMIC: COSV70884489;