rs7581004

Variant names:

• chr2-195009572-G-A
• rs7581004
• ENST00000418387.1:n.147-4980C>T

Variant summary

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

The ENST00000418387.1(ENSG00000235056):​n.147-4980C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 151,192 control chromosomes in the GnomAD database, including 7,108 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 0.30 (7108 hom., cov: 33)
• Consequence: ENSG00000235056 ENST00000418387.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 3 publications found

Genes affected

ENSG00000235056 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418387.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000235056	ENST00000418387.1	TSL:5	n.147-4980C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45788 AN: 151074 Hom.: 7107 Cov.: 33

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.303 AC: 45812 AN: 151192 Hom.: 7108 Cov.: 33 AF XY: 0.303 AC XY: 22412 AN XY: 73846

African (AFR) AF: 0.354 AC: 14616 AN: 41334

American (AMR) AF: 0.226 AC: 3429 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 882 AN: 3450

East Asian (EAS) AF: 0.218 AC: 1113 AN: 5094

South Asian (SAS) AF: 0.351 AC: 1693 AN: 4818

European-Finnish (FIN) AF: 0.355 AC: 3757 AN: 10570

Middle Eastern (MID) AF: 0.252 AC: 73 AN: 290

European-Non Finnish (NFE) AF: 0.287 AC: 19377 AN: 67468

Other (OTH) AF: 0.292 AC: 613 AN: 2102

Alfa AF: 0.288 Hom.: 9556

Bravo AF: 0.293

Asia WGS AF: 0.296 AC: 1029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	12
DANN	Benign	0.72
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs7581004; hg19: chr2-195874296;