16-7786295-C-A

Variant names:

• chr16-7786295-C-A
• rs3112740
• ENST00000777597.1:n.402+18931G>T

Variant summary

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

The ENST00000777597.1(ENSG00000301273):​n.402+18931G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 150,640 control chromosomes in the GnomAD database, including 1,534 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 0.13 (1534 hom., cov: 29)
• Consequence: ENSG00000301273 ENST00000777597.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182
• Publications: 11 publications found

Genes affected

ENSG00000301273 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 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
ENSG00000301273	ENST00000777597.1	n.402+18931G>T		intron_variant	Intron 3 of 3
ENSG00000301273	ENST00000777598.1	n.310+18931G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19615 AN: 150532 Hom.: 1537 Cov.: 29

Gnomad AFR AF: 0.0870

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0870

Gnomad ASJ AF: 0.0727

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.130 AC: 19612 AN: 150640 Hom.: 1534 Cov.: 29 AF XY: 0.133 AC XY: 9774 AN XY: 73446

African (AFR) AF: 0.0870 AC: 3569 AN: 41024

American (AMR) AF: 0.0868 AC: 1315 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.0727 AC: 252 AN: 3464

East Asian (EAS) AF: 0.320 AC: 1626 AN: 5078

South Asian (SAS) AF: 0.168 AC: 800 AN: 4748

European-Finnish (FIN) AF: 0.230 AC: 2335 AN: 10134

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.139 AC: 9408 AN: 67750

Other (OTH) AF: 0.118 AC: 245 AN: 2084

Alfa AF: 0.132 Hom.: 6505

Bravo AF: 0.118

Asia WGS AF: 0.212 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.5
DANN	Benign	0.24
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs3112740; hg19: chr16-7836297;