rs10038971

Variant names:

• chr5-155096973-T-A
• rs10038971
• ENST00000660390.1:n.281+9263T>A

Your query was ambiguous. Multiple possible variants found:

• chr5-155096973-T-A
• chr5-155096973-T-C
• chr5-155096973-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000660390.1(ENSG00000287963):​n.281+9263T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,088 control chromosomes in the GnomAD database, including 12,104 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 0.36 (12104 hom., cov: 32)
• Consequence: ENSG00000287963 ENST00000660390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

Genes affected

ENSG00000287963 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 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
ENSG00000287963	ENST00000660390.1	n.281+9263T>A		intron_variant	Intron 1 of 1
ENSG00000287963	ENST00000668848.1	n.179+9263T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55218 AN: 151970 Hom.: 12070 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.364 AC: 55300 AN: 152088 Hom.: 12104 Cov.: 32 AF XY: 0.367 AC XY: 27273 AN XY: 74362

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.349

Alfa AF: 0.316 Hom.: 1123

Bravo AF: 0.369

Asia WGS AF: 0.391 AC: 1358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	14
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10038971; hg19: chr5-154476533;