rs10507038

Variant names:

• chr12-94509493-G-C
• rs10507038
• XR_945224.3:n.215-29395G>C

Your query was ambiguous. Multiple possible variants found:

• chr12-94509493-G-C
• chr12-94509493-G-T

Variant summary

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

The XR_945224.3(LOC102724960):​n.215-29395G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 151,948 control chromosomes in the GnomAD database, including 19,582 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 0.50 (19582 hom., cov: 31)
• Consequence: LOC102724960 XR_945224.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 0 publications found

Genes affected

LOC102724960 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724960	XR_945224.3	n.215-29395G>C		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75597 AN: 151830 Hom.: 19584 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.498 AC: 75606 AN: 151948 Hom.: 19582 Cov.: 31 AF XY: 0.492 AC XY: 36544 AN XY: 74246

African (AFR) AF: 0.380 AC: 15758 AN: 41448

American (AMR) AF: 0.488 AC: 7458 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1882 AN: 3466

East Asian (EAS) AF: 0.263 AC: 1362 AN: 5170

South Asian (SAS) AF: 0.383 AC: 1840 AN: 4810

European-Finnish (FIN) AF: 0.506 AC: 5326 AN: 10520

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.591 AC: 40148 AN: 67948

Other (OTH) AF: 0.530 AC: 1119 AN: 2112

Alfa AF: 0.403 Hom.: 1135

Bravo AF: 0.491

Asia WGS AF: 0.299 AC: 1043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.2
DANN	Benign	0.76
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs10507038; hg19: chr12-94903269;