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 XR_007088699.1(LOC105376755):​n.265+49863C>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: LOC105376755 XR_007088699.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376755	XR_007088699.1	n.265+49863C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235056	ENST00000418387.1	n.147-4980C>T		intron_variant	Intron 1 of 1	5

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 v4.3

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;