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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775347.1. 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
	ENSG00000300984	ENST00000775347.1		n.290+75029G>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2908740;

hg19: chr7-12059250;