rs964055

Variant names:

• chr16-31975763-C-T
• rs964055
• ENST00000831886.1:n.393-304G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000831886.1(ENSG00000308135):​n.393-304G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000986 in 1,216,836 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00016 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000090 (0 hom.)
• Consequence: ENSG00000308135 ENST00000831886.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 1 publications found

Genes affected

ENSG00000308135 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

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
ENSG00000308135	ENST00000831886.1	n.393-304G>A		intron_variant	Intron 1 of 1
ENSG00000260628	ENST00000568208.6	n.-40C>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.000158 AC: 24 AN: 151816 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000727

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000328

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.0000943

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000132

Gnomad OTH AF: 0.00145

GnomAD4 exome AF: 0.0000901 AC: 96 AN: 1065020 Hom.: 0 Cov.: 15 AF XY: 0.0000779 AC XY: 41 AN XY: 526070

African (AFR) AF: 0.000575 AC: 13 AN: 22626

American (AMR) AF: 0.000438 AC: 9 AN: 20558

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17532

East Asian (EAS) AF: 0.000120 AC: 4 AN: 33230

South Asian (SAS) AF: 0.000119 AC: 7 AN: 58728

European-Finnish (FIN) AF: 0.0000472 AC: 2 AN: 42346

Middle Eastern (MID) AF: 0.000315 AC: 1 AN: 3178

European-Non Finnish (NFE) AF: 0.0000657 AC: 54 AN: 821406

Other (OTH) AF: 0.000132 AC: 6 AN: 45416

GnomAD4 genome AF: 0.000158 AC: 24 AN: 151816 Hom.: 0 Cov.: 31 AF XY: 0.000135 AC XY: 10 AN XY: 74112

African (AFR) AF: 0.0000727 AC: 3 AN: 41260

American (AMR) AF: 0.000328 AC: 5 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3464

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5144

South Asian (SAS) AF: 0.000415 AC: 2 AN: 4816

European-Finnish (FIN) AF: 0.0000943 AC: 1 AN: 10602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.000132 AC: 9 AN: 67974

Other (OTH) AF: 0.00145 AC: 3 AN: 2074

Alfa AF: 0.0000540 Hom.: 0

Bravo AF: 0.000196

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.54
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs964055; hg19: chr16-31987084;