rs2040868

Variant names:

• chr7-45287404-G-A
• rs2040868
• ENST00000666999.1:n.837+17887G>A

Variant summary

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

The ENST00000666999.1(ENSG00000286738):​n.837+17887G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 151,886 control chromosomes in the GnomAD database, including 7,894 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 0.32 (7894 hom., cov: 31)
• Consequence: ENSG00000286738 ENST00000666999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 0 publications found

Genes affected

ENSG00000286738 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286738	ENST00000666999.1	n.837+17887G>A		intron_variant	Intron 1 of 1
ENSG00000303071	ENST00000791567.1	n.51-18880G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48500 AN: 151766 Hom.: 7894 Cov.: 31

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.319 AC: 48527 AN: 151886 Hom.: 7894 Cov.: 31 AF XY: 0.320 AC XY: 23726 AN XY: 74230

African (AFR) AF: 0.308 AC: 12766 AN: 41392

American (AMR) AF: 0.338 AC: 5160 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1264 AN: 3468

East Asian (EAS) AF: 0.145 AC: 749 AN: 5174

South Asian (SAS) AF: 0.368 AC: 1770 AN: 4812

European-Finnish (FIN) AF: 0.283 AC: 2982 AN: 10548

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22622 AN: 67914

Other (OTH) AF: 0.359 AC: 757 AN: 2108

Alfa AF: 0.334 Hom.: 8208

Bravo AF: 0.323

Asia WGS AF: 0.280 AC: 976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.6
DANN	Benign	0.40
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2040868; hg19: chr7-45327003;