4-121609932-T-C

Variant names:

• chr4-121609932-T-C
• rs3811746
• ENST00000807564.1:n.200-15085T>C

Variant summary

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

The ENST00000807564.1(ENSG00000304990):​n.200-15085T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,262 control chromosomes in the GnomAD database, including 1,270 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 (1270 hom., cov: 33)
• Consequence: ENSG00000304990 ENST00000807564.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.723
• Publications: 0 publications found

Genes affected

ENSG00000304990 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.212 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
ENSG00000304990	ENST00000807564.1	n.200-15085T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17704 AN: 152144 Hom.: 1271 Cov.: 33

Gnomad AFR AF: 0.0426

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.116 AC: 17696 AN: 152262 Hom.: 1270 Cov.: 33 AF XY: 0.118 AC XY: 8772 AN XY: 74442

African (AFR) AF: 0.0424 AC: 1761 AN: 41564

American (AMR) AF: 0.150 AC: 2296 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 351 AN: 3466

East Asian (EAS) AF: 0.223 AC: 1157 AN: 5188

South Asian (SAS) AF: 0.171 AC: 826 AN: 4822

European-Finnish (FIN) AF: 0.142 AC: 1509 AN: 10604

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9451 AN: 68008

Other (OTH) AF: 0.123 AC: 261 AN: 2114

Alfa AF: 0.132 Hom.: 182

Bravo AF: 0.114

Asia WGS AF: 0.189 AC: 655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.5
DANN	Benign	0.64
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs3811746; hg19: chr4-122531087;