rs1764424

Positions:

• chr13-95394928-G-C
• chr13-95394928-G-T

Variant summary

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

The XR_007063839.1(LOC124903193):​n.764+9397C>G 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 0.393 in 151,632 control chromosomes in the GnomAD database, including 13,749 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 0.39 (13749 hom., cov: 28)
• Consequence: LOC124903193 XR_007063839.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312

Genes affected

LOC124903193 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903193	XR_007063839.1	n.764+9397C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59528 AN: 151514 Hom.: 13751 Cov.: 28

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.393 AC: 59548 AN: 151632 Hom.: 13749 Cov.: 28 AF XY: 0.393 AC XY: 29093 AN XY: 74034

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.411

Alfa AF: 0.439 Hom.: 1943

Bravo AF: 0.382

Asia WGS AF: 0.392 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.5
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1764424; hg19: chr13-96047182;