16-7753015-C-T

Variant names:

• chr16-7753015-C-T
• rs10492756
• ENST00000777597.1:n.402+52211G>A

Variant summary

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

The ENST00000777597.1(ENSG00000301273):​n.402+52211G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 114,878 control chromosomes in the GnomAD database, including 635 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 0.12 (635 hom., cov: 30)
• Consequence: ENSG00000301273 ENST00000777597.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000777597.1. 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
	ENSG00000301273	ENST00000777597.1		n.402+52211G>A		intron	N/A
	ENSG00000301273	ENST00000777598.1		n.310+52211G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.119 AC: 13677 AN: 114786 Hom.: 634 Cov.: 30

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.0583

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.00873

Gnomad SAS AF: 0.0872

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.110

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.119 AC: 13704 AN: 114878 Hom.: 635 Cov.: 30 AF XY: 0.119 AC XY: 6652 AN XY: 55666

African (AFR) AF: 0.146 AC: 3332 AN: 22894

American (AMR) AF: 0.0812 AC: 962 AN: 11844

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 466 AN: 3194

East Asian (EAS) AF: 0.00875 AC: 23 AN: 2630

South Asian (SAS) AF: 0.0869 AC: 322 AN: 3706

European-Finnish (FIN) AF: 0.179 AC: 1413 AN: 7880

Middle Eastern (MID) AF: 0.123 AC: 33 AN: 268

European-Non Finnish (NFE) AF: 0.116 AC: 6930 AN: 59876

Other (OTH) AF: 0.101 AC: 171 AN: 1694

Alfa AF: 0.101 Hom.: 698

Bravo AF: 0.0838

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.74
DANN	Benign	0.21
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: rs10492756;

hg19: chr16-7803017;