rs7612441

Variant names:

• chr3-66597738-C-T
• rs7612441
• ENST00000735557.1:n.58-7991C>T

Variant summary

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

The ENST00000735557.1(ENSG00000296028):​n.58-7991C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,078 control chromosomes in the GnomAD database, including 4,533 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 0.23 (4533 hom., cov: 32)
• Consequence: ENSG00000296028 ENST00000735557.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635
• Publications: 3 publications found

Genes affected

ENSG00000296028 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000735557.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296028	ENST00000735557.1		n.58-7991C>T		intron	N/A
	ENSG00000296028	ENST00000735558.1		n.113-7991C>T		intron	N/A
	ENSG00000296028	ENST00000735559.1		n.73-7991C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34438 AN: 151960 Hom.: 4535 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.0462

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.226 AC: 34442 AN: 152078 Hom.: 4533 Cov.: 32 AF XY: 0.223 AC XY: 16569 AN XY: 74336

African (AFR) AF: 0.118 AC: 4892 AN: 41478

American (AMR) AF: 0.226 AC: 3456 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1125 AN: 3464

East Asian (EAS) AF: 0.0463 AC: 240 AN: 5178

South Asian (SAS) AF: 0.174 AC: 838 AN: 4816

European-Finnish (FIN) AF: 0.249 AC: 2634 AN: 10578

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20386 AN: 67956

Other (OTH) AF: 0.240 AC: 507 AN: 2114

Alfa AF: 0.281 Hom.: 10593

Bravo AF: 0.221

Asia WGS AF: 0.0980 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.7
DANN	Benign	0.70
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs7612441; hg19: chr3-66648162;