rs10515621

Variant names:

• chr5-148866981-T-C
• rs10515621
• ENST00000798472.1:n.377-5523T>C

Variant summary

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

The ENST00000798472.1(ENSG00000303969):​n.377-5523T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,220 control chromosomes in the GnomAD database, including 1,135 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 0.11 (1135 hom., cov: 32)
• Consequence: ENSG00000303969 ENST00000798472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305
• Publications: 5 publications found

Genes affected

ENSG00000303969 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 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
ENSG00000303969	ENST00000798472.1	n.377-5523T>C		intron_variant	Intron 3 of 4
ENSG00000303969	ENST00000798473.1	n.350-5523T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16086 AN: 152102 Hom.: 1134 Cov.: 32

Gnomad AFR AF: 0.0274

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.0994

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0371

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.106 AC: 16082 AN: 152220 Hom.: 1135 Cov.: 32 AF XY: 0.103 AC XY: 7648 AN XY: 74414

African (AFR) AF: 0.0274 AC: 1137 AN: 41550

American (AMR) AF: 0.0992 AC: 1517 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 513 AN: 3470

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5166

South Asian (SAS) AF: 0.0369 AC: 178 AN: 4824

European-Finnish (FIN) AF: 0.147 AC: 1562 AN: 10592

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10807 AN: 68016

Other (OTH) AF: 0.118 AC: 250 AN: 2112

Alfa AF: 0.141 Hom.: 875

Bravo AF: 0.102

Asia WGS AF: 0.0200 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.58
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs10515621; hg19: chr5-148246544;