rs10487438

Variant names:

• chr7-126208272-G-C
• rs10487438
• ENST00000809641.1:n.145-25265G>C

Variant summary

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

The ENST00000809641.1(ENSG00000305210):​n.145-25265G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0874 in 152,044 control chromosomes in the GnomAD database, including 868 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 0.087 (868 hom., cov: 32)
• Consequence: ENSG00000305210 ENST00000809641.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 1 publications found

Genes affected

ENSG00000305210 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 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
ENSG00000305210	ENST00000809641.1	n.145-25265G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0873 AC: 13260 AN: 151926 Hom.: 865 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0492

Gnomad ASJ AF: 0.0447

Gnomad EAS AF: 0.0832

Gnomad SAS AF: 0.0442

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0386

Gnomad OTH AF: 0.0822

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

GnomAD4 genome AF: 0.0874 AC: 13288 AN: 152044 Hom.: 868 Cov.: 32 AF XY: 0.0896 AC XY: 6653 AN XY: 74290

African (AFR) AF: 0.185 AC: 7656 AN: 41494

American (AMR) AF: 0.0492 AC: 749 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.0447 AC: 155 AN: 3464

East Asian (EAS) AF: 0.0827 AC: 427 AN: 5166

South Asian (SAS) AF: 0.0442 AC: 213 AN: 4820

European-Finnish (FIN) AF: 0.113 AC: 1197 AN: 10592

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0386 AC: 2624 AN: 67958

Other (OTH) AF: 0.0818 AC: 173 AN: 2114

Alfa AF: 0.0666 Hom.: 83

Bravo AF: 0.0884

Asia WGS AF: 0.0690 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.60
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10487438; hg19: chr7-125848326;