rs2908740

Variant names:

• chr7-12019624-C-A
• rs2908740
• ENST00000775347.1:n.290+75029G>T

Variant summary

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

The ENST00000775347.1(ENSG00000300984):​n.290+75029G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 151,660 control chromosomes in the GnomAD database, including 12,221 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 0.39 (12221 hom., cov: 30)
• Consequence: ENSG00000300984 ENST00000775347.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.521
• Publications: 1 publications found

Genes affected

ENSG00000300984 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901589	XR_007060211.1	n.85+75029G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300984	ENST00000775347.1	n.290+75029G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59723 AN: 151540 Hom.: 12188 Cov.: 30

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.375

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.394 AC: 59807 AN: 151660 Hom.: 12221 Cov.: 30 AF XY: 0.392 AC XY: 29041 AN XY: 74064

African (AFR) AF: 0.507 AC: 20979 AN: 41344

American (AMR) AF: 0.366 AC: 5581 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1686 AN: 3464

East Asian (EAS) AF: 0.240 AC: 1242 AN: 5172

South Asian (SAS) AF: 0.374 AC: 1798 AN: 4812

European-Finnish (FIN) AF: 0.368 AC: 3838 AN: 10436

Middle Eastern (MID) AF: 0.369 AC: 107 AN: 290

European-Non Finnish (NFE) AF: 0.348 AC: 23617 AN: 67890

Other (OTH) AF: 0.386 AC: 812 AN: 2104

Alfa AF: 0.380 Hom.: 1424

Bravo AF: 0.399

Asia WGS AF: 0.334 AC: 1160 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.3
DANN	Benign	0.17
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs2908740; hg19: chr7-12059250;