7-35361837-T-C

Variant names:

• chr7-35361837-T-C
• rs2392362
• ENST00000656715.1:n.204+9446T>C

Variant summary

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

The ENST00000656715.1(ENSG00000287651):​n.204+9446T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.726 in 151,842 control chromosomes in the GnomAD database, including 40,417 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 0.73 (40417 hom., cov: 30)
• Consequence: ENSG00000287651 ENST00000656715.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310
• Publications: 10 publications found

Genes affected

ENSG00000287651 (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 (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC401324	NR_038864.1	n.187+9446T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287651	ENST00000656715.1	n.204+9446T>C		intron_variant	Intron 2 of 2
ENSG00000287651	ENST00000768394.1	n.267+9446T>C		intron_variant	Intron 2 of 2
ENSG00000287651	ENST00000768395.1	n.133-14717T>C		intron_variant	Intron 1 of 1
ENSG00000287651	ENST00000768396.1	n.101+9446T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.726 AC: 110191 AN: 151724 Hom.: 40393 Cov.: 30

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.726 AC: 110266 AN: 151842 Hom.: 40417 Cov.: 30 AF XY: 0.724 AC XY: 53742 AN XY: 74198

African (AFR) AF: 0.812 AC: 33628 AN: 41404

American (AMR) AF: 0.682 AC: 10408 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2293 AN: 3466

East Asian (EAS) AF: 0.837 AC: 4319 AN: 5158

South Asian (SAS) AF: 0.691 AC: 3317 AN: 4802

European-Finnish (FIN) AF: 0.680 AC: 7146 AN: 10502

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46957 AN: 67932

Other (OTH) AF: 0.697 AC: 1472 AN: 2112

Alfa AF: 0.705 Hom.: 91648

Bravo AF: 0.727

Asia WGS AF: 0.738 AC: 2565 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	5.9
DANN	Benign	0.78
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs2392362; hg19: chr7-35401447;