rs7652214

Variant names:

• chr3-120471149-G-C
• rs7652214
• ENST00000659560.1:n.179+21997G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000659560.1(ENSG00000286735):​n.179+21997G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0105 in 152,268 control chromosomes in the GnomAD database, including 15 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 0.011 (15 hom., cov: 32)
• Consequence: ENSG00000286735 ENST00000659560.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.16
• Publications: 1 publications found

Genes affected

ENSG00000286735 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0105 (1601/152268) while in subpopulation AMR AF = 0.0166 (254/15302). AF 95% confidence interval is 0.0157. There are 15 homozygotes in GnomAd4. There are 673 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 15 gene

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
ENSG00000286735	ENST00000659560.1	n.179+21997G>C		intron_variant	Intron 1 of 2
ENSG00000286735	ENST00000732215.1	n.95+21988G>C		intron_variant	Intron 1 of 3
ENSG00000286735	ENST00000732216.1	n.172+21988G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0105 AC: 1601 AN: 152150 Hom.: 15 Cov.: 32

Gnomad AFR AF: 0.00381

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0166

Gnomad ASJ AF: 0.00375

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.0144

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

GnomAD4 genome AF: 0.0105 AC: 1601 AN: 152268 Hom.: 15 Cov.: 32 AF XY: 0.00904 AC XY: 673 AN XY: 74452

African (AFR) AF: 0.00380 AC: 158 AN: 41544

American (AMR) AF: 0.0166 AC: 254 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00375 AC: 13 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.00 AC: 0 AN: 4824

European-Finnish (FIN) AF: 0.00104 AC: 11 AN: 10608

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0165 AC: 1119 AN: 68020

Other (OTH) AF: 0.0142 AC: 30 AN: 2112

Alfa AF: 0.0124 Hom.: 2

Bravo AF: 0.0123

Asia WGS AF: 0.000578 AC: 2 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	13
DANN	Benign	0.42
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs7652214; hg19: chr3-120189996;