rs2323476

Positions:

• chr13-37391947-G-A
• chr13-37391947-G-C
• chr13-37391947-G-T

Variant summary

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

The XR_007063761.1(LOC124903159):​n.243+27797G>A 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 0.425 in 152,052 control chromosomes in the GnomAD database, including 14,830 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 0.42 (14830 hom., cov: 32)
• Consequence: LOC124903159 XR_007063761.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758

Genes affected

LOC124903159 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903159	XR_007063761.1	n.243+27797G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64570 AN: 151936 Hom.: 14818 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.425 AC: 64600 AN: 152052 Hom.: 14830 Cov.: 32 AF XY: 0.435 AC XY: 32347 AN XY: 74298

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.785

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.449

Alfa AF: 0.452 Hom.: 7416

Bravo AF: 0.422

Asia WGS AF: 0.652 AC: 2265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.18
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2323476; hg19: chr13-37966084;