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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000831886.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308135	ENST00000831886.1		n.393-304G>A		intron	N/A
	ENSG00000260628	ENST00000568208.6	TSL:6	n.-40C>T		upstream_gene	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs964055;

hg19: chr16-31987084;