rs10507038

chr12-94509493-G-Cchr12-94509493-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_945224.3(LOC102724960):n.215-29395G>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

Genes affected

LOC102724960 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC102724960	XR_945224.3	n.215-29395G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.530

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507038; hg19: chr12-94903269;