3-40771486-T-C

Variant names:

• chr3-40771486-T-C
• rs592275
• ENST00000412811.1:n.147-2382T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000412811.1(ENSG00000231873):​n.147-2382T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.83 in 152,234 control chromosomes in the GnomAD database, including 55,041 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 (55041 hom., cov: 33)
• Consequence: ENSG00000231873 ENST00000412811.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266

Genes affected

ENSG00000231873 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377043	XR_007095883.1	n.147-2382T>C		intron_variant	Intron 1 of 3
LOC105377043	XR_007095884.1	n.147-2382T>C		intron_variant	Intron 1 of 2
LOC105377043	XR_007095885.1	n.147-2382T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231873	ENST00000412811.1	n.147-2382T>C		intron_variant	Intron 1 of 2	4
ENSG00000231873	ENST00000665970.1	n.58-2382T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126386 AN: 152116 Hom.: 55031 Cov.: 33

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.830 AC: 126426 AN: 152234 Hom.: 55041 Cov.: 33 AF XY: 0.834 AC XY: 62068 AN XY: 74434

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.917

Gnomad4 ASJ AF: 0.930

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.933

Gnomad4 FIN AF: 0.914

Gnomad4 NFE AF: 0.947

Gnomad4 OTH AF: 0.865

Alfa AF: 0.853 Hom.: 10741

Bravo AF: 0.817

Asia WGS AF: 0.928 AC: 3228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs592275; hg19: chr3-40812977;