rs16949665

Variant names:

• chr15-94905185-G-A
• rs16949665
• ENST00000614581.1:n.237+618G>A

Variant summary

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

The ENST00000618611.4(ENSG00000277654):​n.193+63934G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0448 in 152,120 control chromosomes in the GnomAD database, including 430 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 0.045 (430 hom., cov: 32)
• Consequence: ENSG00000277654 ENST00000618611.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122

Genes affected

ENSG00000277654 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000277654	ENST00000614581.1	n.237+618G>A		intron_variant	Intron 3 of 4	5
ENSG00000277654	ENST00000615751.4	n.74+48322G>A		intron_variant	Intron 1 of 4	5
ENSG00000277654	ENST00000618377.1	n.330+48322G>A		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.0448 AC: 6809 AN: 152002 Hom.: 431 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0172

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.00472

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00857

Gnomad OTH AF: 0.0292

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

GnomAD4 genome AF: 0.0448 AC: 6816 AN: 152120 Hom.: 430 Cov.: 32 AF XY: 0.0431 AC XY: 3202 AN XY: 74370

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.0171

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00104

Gnomad4 FIN AF: 0.00472

Gnomad4 NFE AF: 0.00857

Gnomad4 OTH AF: 0.0289

Alfa AF: 0.0367 Hom.: 54

Bravo AF: 0.0514

Asia WGS AF: 0.00606 AC: 22 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	12
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16949665; hg19: chr15-95448414;