7-41582932-G-T

Variant names:

• chr7-41582932-G-T
• rs4724055
• ENST00000840095.1:n.157-3370G>T

Variant summary

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

The ENST00000840095.1(ENSG00000309289):​n.157-3370G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.931 in 152,262 control chromosomes in the GnomAD database, including 66,179 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 0.93 (66179 hom., cov: 33)
• Consequence: ENSG00000309289 ENST00000840095.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 3 publications found

Genes affected

ENSG00000309289 (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 (NFE) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000840095.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309289	ENST00000840095.1		n.157-3370G>T		intron	N/A
	ENSG00000309316	ENST00000840245.1		n.56+3260C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.931 AC: 141697 AN: 152144 Hom.: 66154 Cov.: 33

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.925

Gnomad ASJ AF: 0.958

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.984

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.968

Gnomad OTH AF: 0.937

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

GnomAD4 genome AF: 0.931 AC: 141771 AN: 152262 Hom.: 66179 Cov.: 33 AF XY: 0.930 AC XY: 69228 AN XY: 74454

African (AFR) AF: 0.865 AC: 35915 AN: 41514

American (AMR) AF: 0.926 AC: 14167 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.958 AC: 3327 AN: 3472

East Asian (EAS) AF: 0.887 AC: 4593 AN: 5178

South Asian (SAS) AF: 0.903 AC: 4350 AN: 4818

European-Finnish (FIN) AF: 0.984 AC: 10453 AN: 10624

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.968 AC: 65833 AN: 68034

Other (OTH) AF: 0.937 AC: 1979 AN: 2112

Alfa AF: 0.951 Hom.: 57368

Bravo AF: 0.923

Asia WGS AF: 0.893 AC: 3105 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.62
PhyloP100		0.036

Splicing

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

Other links and lift over

dbSNP: rs4724055; hg19: chr7-41622530;