rs7620754

Variant names:

• chr3-114229128-T-C
• rs7620754
• ENST00000481773.2:n.239-4214T>C

Variant summary

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

The ENST00000481773.2(ENSG00000241490):​n.239-4214T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 151,846 control chromosomes in the GnomAD database, including 4,635 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 0.24 (4635 hom., cov: 31)
• Consequence: ENSG00000241490 ENST00000481773.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920
• Publications: 6 publications found

Genes affected

ENSG00000241490 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 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
ENSG00000241490	ENST00000481773.2	n.239-4214T>C		intron_variant	Intron 1 of 2	3
ENSG00000241490	ENST00000493033.1	n.161-4214T>C		intron_variant	Intron 1 of 1	2
ENSG00000241490	ENST00000779676.1	n.342-4214T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36817 AN: 151728 Hom.: 4630 Cov.: 31

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.243 AC: 36834 AN: 151846 Hom.: 4635 Cov.: 31 AF XY: 0.247 AC XY: 18364 AN XY: 74234

African (AFR) AF: 0.230 AC: 9543 AN: 41410

American (AMR) AF: 0.271 AC: 4129 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 919 AN: 3466

East Asian (EAS) AF: 0.326 AC: 1677 AN: 5152

South Asian (SAS) AF: 0.318 AC: 1532 AN: 4824

European-Finnish (FIN) AF: 0.264 AC: 2781 AN: 10516

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15463 AN: 67908

Other (OTH) AF: 0.260 AC: 548 AN: 2106

Alfa AF: 0.238 Hom.: 7650

Bravo AF: 0.243

Asia WGS AF: 0.303 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.47
PhyloP100		0.092

Splicing

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

Other links and lift over

dbSNP: rs7620754; hg19: chr3-113947975;