chr4-176929369-A-G

Variant names:

• chr4-176929369-A-G
• rs721684
• ENST00000656694.1:n.347-35464T>C

Variant summary

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

The ENST00000656694.1(ENSG00000287544):​n.347-35464T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 151,902 control chromosomes in the GnomAD database, including 39,510 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 0.67 (39510 hom., cov: 33)
• Consequence: ENSG00000287544 ENST00000656694.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 2 publications found

Genes affected

ENSG00000287544 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 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
ENSG00000287544	ENST00000656694.1	n.347-35464T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102204 AN: 151784 Hom.: 39501 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.673 AC: 102228 AN: 151902 Hom.: 39510 Cov.: 33 AF XY: 0.675 AC XY: 50137 AN XY: 74242

African (AFR) AF: 0.260 AC: 10770 AN: 41450

American (AMR) AF: 0.748 AC: 11395 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2698 AN: 3466

East Asian (EAS) AF: 0.962 AC: 4971 AN: 5168

South Asian (SAS) AF: 0.699 AC: 3369 AN: 4820

European-Finnish (FIN) AF: 0.836 AC: 8812 AN: 10540

Middle Eastern (MID) AF: 0.705 AC: 206 AN: 292

European-Non Finnish (NFE) AF: 0.849 AC: 57688 AN: 67912

Other (OTH) AF: 0.707 AC: 1488 AN: 2106

Alfa AF: 0.699 Hom.: 5641

Bravo AF: 0.652

Asia WGS AF: 0.808 AC: 2806 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.5
DANN	Benign	0.43
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs721684; hg19: chr4-177850523;