rs10491372

Variant names:

• chr5-29955328-G-A
• rs10491372
• XR_001742505.1:n.341+2293C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-29955328-G-A
• chr5-29955328-G-T

Variant summary

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

The XR_001742505.1(LOC105374705):​n.341+2293C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0233 in 152,222 control chromosomes in the GnomAD database, including 92 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 0.023 (92 hom., cov: 32)
• Consequence: LOC105374705 XR_001742505.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179

Genes affected

LOC105374705 (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 = 0.0587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374705	XR_001742505.1	n.341+2293C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0233 AC: 3550 AN: 152104 Hom.: 92 Cov.: 32

Gnomad AFR AF: 0.0608

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.0115

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00269

Gnomad FIN AF: 0.00283

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0108

Gnomad OTH AF: 0.0225

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

GnomAD4 genome AF: 0.0233 AC: 3553 AN: 152222 Hom.: 92 Cov.: 32 AF XY: 0.0220 AC XY: 1640 AN XY: 74416

Gnomad4 AFR AF: 0.0607 AC: 0.0606885 AN: 0.0606885

Gnomad4 AMR AF: 0.0114 AC: 0.0114454 AN: 0.0114454

Gnomad4 ASJ AF: 0.00749 AC: 0.00748848 AN: 0.00748848

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.00270 AC: 0.00269598 AN: 0.00269598

Gnomad4 FIN AF: 0.00283 AC: 0.00283072 AN: 0.00283072

Gnomad4 NFE AF: 0.0108 AC: 0.0108066 AN: 0.0108066

Gnomad4 OTH AF: 0.0218 AC: 0.0218009 AN: 0.0218009

Alfa AF: 0.00131 Hom.: 1

Bravo AF: 0.0259

Asia WGS AF: 0.00549 AC: 19 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	1.6
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491372; hg19: chr5-29955435;