chr15-78621642-A-C

Variant names:

• chr15-78621642-A-C
• rs12911814
• ENST00000821537.1:n.210+1332A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000821537.1(ENSG00000259555):​n.210+1332A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0307 in 151,352 control chromosomes in the GnomAD database, including 105 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 0.031 (105 hom., cov: 32)
• Consequence: ENSG00000259555 ENST00000821537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.387
• Publications: 2 publications found

Genes affected

ENSG00000259555 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0307 (4641/151352) while in subpopulation NFE AF = 0.0494 (3353/67916). AF 95% confidence interval is 0.048. There are 105 homozygotes in GnomAd4. There are 2151 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 105 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821537.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259555	ENST00000821537.1		n.210+1332A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0307 AC: 4640 AN: 151236 Hom.: 105 Cov.: 32

Gnomad AFR AF: 0.0113

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0217

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.000208

Gnomad SAS AF: 0.0150

Gnomad FIN AF: 0.0267

Gnomad MID AF: 0.0224

Gnomad NFE AF: 0.0493

Gnomad OTH AF: 0.0293

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

GnomAD4 genome AF: 0.0307 AC: 4641 AN: 151352 Hom.: 105 Cov.: 32 AF XY: 0.0291 AC XY: 2151 AN XY: 73980

African (AFR) AF: 0.0113 AC: 468 AN: 41300

American (AMR) AF: 0.0216 AC: 329 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3468

East Asian (EAS) AF: 0.000209 AC: 1 AN: 4788

South Asian (SAS) AF: 0.0150 AC: 72 AN: 4798

European-Finnish (FIN) AF: 0.0267 AC: 282 AN: 10564

Middle Eastern (MID) AF: 0.0207 AC: 6 AN: 290

European-Non Finnish (NFE) AF: 0.0494 AC: 3353 AN: 67916

Other (OTH) AF: 0.0290 AC: 61 AN: 2106

Alfa AF: 0.0374 Hom.: 15

Bravo AF: 0.0295

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.89
DANN	Benign	0.17
PhyloP100		0.39
PromoterAI		0.0059	Neutral

Splicing

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

Other links and lift over

dbSNP: rs12911814; hg19: chr15-78913984;