chr15-94775538-T-C

Variant names:

• chr15-94775538-T-C
• rs16949516
• ENST00000722729.1:n.359-9521A>G

Variant summary

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

The ENST00000722729.1(ENSG00000294319):​n.359-9521A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,110 control chromosomes in the GnomAD database, including 3,254 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 0.14 (3254 hom., cov: 33)
• Consequence: ENSG00000294319 ENST00000722729.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70
• Publications: 4 publications found

Genes affected

ENSG00000294319 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722729.1. 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
	ENSG00000294319	ENST00000722729.1		n.359-9521A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21643 AN: 151992 Hom.: 3244 Cov.: 33

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.0958

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.0473

Gnomad SAS AF: 0.0503

Gnomad FIN AF: 0.00867

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0442

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.143 AC: 21678 AN: 152110 Hom.: 3254 Cov.: 33 AF XY: 0.139 AC XY: 10329 AN XY: 74368

African (AFR) AF: 0.379 AC: 15719 AN: 41438

American (AMR) AF: 0.0956 AC: 1462 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3472

East Asian (EAS) AF: 0.0471 AC: 244 AN: 5184

South Asian (SAS) AF: 0.0497 AC: 240 AN: 4826

European-Finnish (FIN) AF: 0.00867 AC: 92 AN: 10606

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0442 AC: 3003 AN: 67974

Other (OTH) AF: 0.127 AC: 269 AN: 2114

Alfa AF: 0.0909 Hom.: 2882

Bravo AF: 0.160

Asia WGS AF: 0.0800 AC: 277 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.034
DANN	Benign	0.83
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs16949516; hg19: chr15-95318767;