chr15-36359637-T-G

Position:

• chr15-36359637-T-G

Variant summary

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

The XR_932108.3(LOC105370767):​n.275+1603A>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 0.657 in 151,996 control chromosomes in the GnomAD database, including 35,427 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 0.66 (35427 hom., cov: 32)
• Consequence: LOC105370767 XR_932108.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.605

Genes affected

LOC105370767 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370767	XR_932108.3	n.275+1603A>C		intron_variant, non_coding_transcript_variant
LOC105370767	XR_932109.2	n.211A>C		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99783 AN: 151878 Hom.: 35420 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.657 AC: 99807 AN: 151996 Hom.: 35427 Cov.: 32 AF XY: 0.664 AC XY: 49318 AN XY: 74286

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.768

Gnomad4 ASJ AF: 0.801

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.854

Gnomad4 FIN AF: 0.738

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.680

Alfa AF: 0.737 Hom.: 58151

Bravo AF: 0.643

Asia WGS AF: 0.896 AC: 3117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4130461; hg19: chr15-36651838;