rs964611

Variant names:

• chr15-48305317-C-A
• rs964611
• ENST00000845644.1:n.65+7964G>T

Your query was ambiguous. Multiple possible variants found:

• chr15-48305317-C-A
• chr15-48305317-C-G
• chr15-48305317-C-T

Variant summary

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

The ENST00000845644.1(ENSG00000309916):​n.65+7964G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,164 control chromosomes in the GnomAD database, including 1,601 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 (1601 hom., cov: 32)
• Consequence: ENSG00000309916 ENST00000845644.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306
• Publications: 18 publications found

Genes affected

ENSG00000309916 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.173 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
ENSG00000309916	ENST00000845644.1	n.65+7964G>T		intron_variant	Intron 1 of 2
ENSG00000309916	ENST00000845646.1	n.56+7964G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21371 AN: 152046 Hom.: 1596 Cov.: 32

Gnomad AFR AF: 0.0994

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.141 AC: 21394 AN: 152164 Hom.: 1601 Cov.: 32 AF XY: 0.139 AC XY: 10354 AN XY: 74410

African (AFR) AF: 0.0993 AC: 4122 AN: 41506

American (AMR) AF: 0.178 AC: 2725 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 663 AN: 3470

East Asian (EAS) AF: 0.115 AC: 597 AN: 5178

South Asian (SAS) AF: 0.177 AC: 854 AN: 4816

European-Finnish (FIN) AF: 0.133 AC: 1410 AN: 10604

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.155 AC: 10546 AN: 67988

Other (OTH) AF: 0.179 AC: 378 AN: 2116

Alfa AF: 0.153 Hom.: 3475

Bravo AF: 0.142

Asia WGS AF: 0.173 AC: 600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.65
DANN	Benign	0.35
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs964611; hg19: chr15-48597514;