chr15-46497624-A-G

Variant names:

• chr15-46497624-A-G
• rs996215
• ENST00000661853.1:n.45+87271A>G

Variant summary

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

The ENST00000661853.1(ENSG00000287704):​n.45+87271A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.924 in 152,232 control chromosomes in the GnomAD database, including 65,406 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 0.92 (65406 hom., cov: 32)
• Consequence: ENSG00000287704 ENST00000661853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 4 publications found

Genes affected

ENSG00000287704 (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 (AFR) allele frequency at 95% confidence interval = 0.975 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
ENSG00000287704	ENST00000661853.1	n.45+87271A>G		intron_variant	Intron 1 of 1
ENSG00000287704	ENST00000686120.1	n.57-80583A>G		intron_variant	Intron 1 of 2
ENSG00000287704	ENST00000736459.1	n.47-80583A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.924 AC: 140597 AN: 152114 Hom.: 65364 Cov.: 32

Gnomad AFR AF: 0.983

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.944

Gnomad OTH AF: 0.920

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

GnomAD4 genome AF: 0.924 AC: 140693 AN: 152232 Hom.: 65406 Cov.: 32 AF XY: 0.916 AC XY: 68193 AN XY: 74432

African (AFR) AF: 0.983 AC: 40864 AN: 41556

American (AMR) AF: 0.819 AC: 12518 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.935 AC: 3241 AN: 3468

East Asian (EAS) AF: 0.706 AC: 3640 AN: 5156

South Asian (SAS) AF: 0.756 AC: 3642 AN: 4820

European-Finnish (FIN) AF: 0.894 AC: 9481 AN: 10600

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.944 AC: 64237 AN: 68026

Other (OTH) AF: 0.917 AC: 1934 AN: 2110

Alfa AF: 0.924 Hom.: 11069

Bravo AF: 0.920

Asia WGS AF: 0.739 AC: 2571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.3
DANN	Benign	0.70
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs996215; hg19: chr15-46789822;