7-41189487-T-C

Variant names:

• chr7-41189487-T-C
• rs255012
• ENST00000790149.1:n.73+33220A>G

Variant summary

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

The ENST00000790149.1(ENSG00000302868):​n.73+33220A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.741 in 151,836 control chromosomes in the GnomAD database, including 42,166 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 0.74 (42166 hom., cov: 30)
• Consequence: ENSG00000302868 ENST00000790149.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.896
• Publications: 1 publications found

Genes affected

ENSG00000302868 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.823 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
ENSG00000302868	ENST00000790149.1	n.73+33220A>G		intron_variant	Intron 1 of 3
ENSG00000302900	ENST00000790334.1	n.214-32868A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.741 AC: 112430 AN: 151722 Hom.: 42140 Cov.: 30

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.741 AC: 112511 AN: 151836 Hom.: 42166 Cov.: 30 AF XY: 0.747 AC XY: 55424 AN XY: 74194

African (AFR) AF: 0.815 AC: 33752 AN: 41418

American (AMR) AF: 0.773 AC: 11807 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2482 AN: 3464

East Asian (EAS) AF: 0.826 AC: 4252 AN: 5148

South Asian (SAS) AF: 0.844 AC: 4064 AN: 4814

European-Finnish (FIN) AF: 0.761 AC: 7971 AN: 10478

Middle Eastern (MID) AF: 0.695 AC: 203 AN: 292

European-Non Finnish (NFE) AF: 0.675 AC: 45882 AN: 67928

Other (OTH) AF: 0.727 AC: 1532 AN: 2108

Alfa AF: 0.699 Hom.: 4283

Bravo AF: 0.742

Asia WGS AF: 0.856 AC: 2975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
DANN	Benign	0.63
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs255012; hg19: chr7-41229085;