15-37120771-A-G

Variant names:

• chr15-37120771-A-G
• rs2381966
• ENST00000770746.1:n.294-12540A>G

Variant summary

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

The ENST00000770746.1(ENSG00000259460):​n.294-12540A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,116 control chromosomes in the GnomAD database, including 5,315 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 0.26 (5315 hom., cov: 33)
• Consequence: ENSG00000259460 ENST00000770746.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.889
• Publications: 5 publications found

Genes affected

ENSG00000259460 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000770746.1. 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
	ENSG00000259460	ENST00000770746.1		n.294-12540A>G		intron	N/A
	ENSG00000259460	ENST00000770747.1		n.183-8142A>G		intron	N/A
	ENSG00000259460	ENST00000770748.1		n.656-8142A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39121 AN: 151998 Hom.: 5312 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.00577

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.257 AC: 39141 AN: 152116 Hom.: 5315 Cov.: 33 AF XY: 0.253 AC XY: 18837 AN XY: 74364

African (AFR) AF: 0.323 AC: 13416 AN: 41480

American (AMR) AF: 0.168 AC: 2569 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 772 AN: 3466

East Asian (EAS) AF: 0.00578 AC: 30 AN: 5190

South Asian (SAS) AF: 0.219 AC: 1058 AN: 4826

European-Finnish (FIN) AF: 0.282 AC: 2979 AN: 10562

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17349 AN: 67976

Other (OTH) AF: 0.221 AC: 468 AN: 2114

Alfa AF: 0.253 Hom.: 2439

Bravo AF: 0.250

Asia WGS AF: 0.107 AC: 376 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	11
DANN	Benign	0.82
PhyloP100		0.89

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2381966;

hg19: chr15-37412972;