rs716556

Variant names:

• chr4-99763644-G-A
• rs716556
• ENST00000795494.1:n.176-3943C>T

Variant summary

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

The ENST00000795494.1(ENSG00000303547):​n.176-3943C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 152,024 control chromosomes in the GnomAD database, including 23,204 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 0.53 (23204 hom., cov: 32)
• Consequence: ENSG00000303547 ENST00000795494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 4 publications found

Genes affected

ENSG00000303547 (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 (NFE) allele frequency at 95% confidence interval = 0.638 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
ENSG00000303547	ENST00000795494.1	n.176-3943C>T		intron_variant	Intron 2 of 2
ENSG00000303547	ENST00000795495.1	n.350-3943C>T		intron_variant	Intron 1 of 1
ENSG00000303547	ENST00000795496.1	n.97-3943C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81214 AN: 151906 Hom.: 23190 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.535 AC: 81263 AN: 152024 Hom.: 23204 Cov.: 32 AF XY: 0.534 AC XY: 39689 AN XY: 74304

African (AFR) AF: 0.327 AC: 13540 AN: 41458

American (AMR) AF: 0.587 AC: 8963 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2414 AN: 3464

East Asian (EAS) AF: 0.387 AC: 1998 AN: 5166

South Asian (SAS) AF: 0.420 AC: 2020 AN: 4810

European-Finnish (FIN) AF: 0.625 AC: 6605 AN: 10574

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.643 AC: 43706 AN: 67960

Other (OTH) AF: 0.583 AC: 1234 AN: 2116

Alfa AF: 0.617 Hom.: 22203

Bravo AF: 0.523

Asia WGS AF: 0.387 AC: 1347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.30
DANN	Benign	0.73
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs716556; hg19: chr4-100684801;