chr7-10081578-T-G

Variant names:

• chr7-10081578-T-G
• rs988418
• ENST00000654800.2:n.219+3698A>C

Variant summary

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

The ENST00000654800.2(ENSG00000287409):​n.219+3698A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 152,188 control chromosomes in the GnomAD database, including 53,220 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 0.83 (53220 hom., cov: 33)
• Consequence: ENSG00000287409 ENST00000654800.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03
• Publications: 3 publications found

Genes affected

ENSG00000287409 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.886 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
ENSG00000287409	ENST00000654800.2	n.219+3698A>C		intron_variant	Intron 1 of 1
ENSG00000287409	ENST00000747458.1	n.206+3698A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126552 AN: 152070 Hom.: 53198 Cov.: 33

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.832 AC: 126624 AN: 152188 Hom.: 53220 Cov.: 33 AF XY: 0.825 AC XY: 61389 AN XY: 74406

African (AFR) AF: 0.801 AC: 33233 AN: 41502

American (AMR) AF: 0.698 AC: 10681 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3045 AN: 3472

East Asian (EAS) AF: 0.555 AC: 2863 AN: 5158

South Asian (SAS) AF: 0.860 AC: 4148 AN: 4824

European-Finnish (FIN) AF: 0.862 AC: 9135 AN: 10598

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.892 AC: 60657 AN: 68018

Other (OTH) AF: 0.842 AC: 1774 AN: 2108

Alfa AF: 0.856 Hom.: 78235

Bravo AF: 0.816

Asia WGS AF: 0.760 AC: 2647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.54
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs988418; hg19: chr7-10121205;