15-36359637-T-G

Variant names:

• chr15-36359637-T-G
• rs4130461
• XR_932109.2:n.211A>C

Variant summary

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

The XR_932109.2(LOC105370767):​n.211A>C variant causes a non coding transcript exon 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_932109.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.605
• Publications: 2 publications found

Genes affected

LOC105370767 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780278.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301624	ENST00000780278.1		n.131+1869A>C		intron	N/A
	ENSG00000301624	ENST00000780279.1		n.275+1603A>C		intron	N/A

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

African (AFR) AF: 0.370 AC: 15338 AN: 41426

American (AMR) AF: 0.768 AC: 11736 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 2778 AN: 3470

East Asian (EAS) AF: 0.997 AC: 5148 AN: 5162

South Asian (SAS) AF: 0.854 AC: 4113 AN: 4818

European-Finnish (FIN) AF: 0.738 AC: 7796 AN: 10564

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.745 AC: 50615 AN: 67966

Other (OTH) AF: 0.680 AC: 1437 AN: 2114

Alfa AF: 0.728 Hom.: 79406

Bravo AF: 0.643

Asia WGS AF: 0.896 AC: 3117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.1
DANN	Benign	0.63
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs4130461; hg19: chr15-36651838;