chr16-13957035-G-A

Variant names:

• chr16-13957035-G-A
• rs11648736
• ENST00000814369.1:n.54G>A

Variant summary

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

The ENST00000814369.1(ENSG00000305960):​n.54G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,852 control chromosomes in the GnomAD database, including 9,616 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 0.35 (9616 hom., cov: 31)
• Consequence: ENSG00000305960 ENST00000814369.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 4 publications found

Genes affected

ENSG00000305960 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 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
ENSG00000305960	ENST00000814369.1	n.54G>A		non_coding_transcript_exon_variant	Exon 1 of 4
ENSG00000305960	ENST00000814382.1	n.329G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000305960	ENST00000814384.1	n.336G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52731 AN: 151734 Hom.: 9584 Cov.: 31

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.348 AC: 52817 AN: 151852 Hom.: 9616 Cov.: 31 AF XY: 0.343 AC XY: 25485 AN XY: 74202

African (AFR) AF: 0.442 AC: 18278 AN: 41386

American (AMR) AF: 0.275 AC: 4203 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1218 AN: 3464

East Asian (EAS) AF: 0.246 AC: 1269 AN: 5150

South Asian (SAS) AF: 0.260 AC: 1246 AN: 4792

European-Finnish (FIN) AF: 0.299 AC: 3145 AN: 10532

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22295 AN: 67944

Other (OTH) AF: 0.360 AC: 758 AN: 2104

Alfa AF: 0.354 Hom.: 1384

Bravo AF: 0.352

Asia WGS AF: 0.310 AC: 1078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.0
DANN	Benign	0.76
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs11648736; hg19: chr16-14050892;