3-42950154-T-G

Variant names:

• chr3-42950154-T-G
• rs704894
• ENST00000446977.2:c.277+8083T>G

Variant summary

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

The ENST00000446977.2(ENSG00000273291):​c.277+8083T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.95 in 152,266 control chromosomes in the GnomAD database, including 68,906 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 0.95 (68906 hom., cov: 32)
• Consequence: ENSG00000273291 ENST00000446977.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 0 publications found

Genes affected

ENSG00000273291 (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 = 0.977 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
ENSG00000273291	ENST00000446977.2	c.277+8083T>G		intron_variant	Intron 4 of 4	4		ENSP00000477043.1
ENSG00000273291	ENST00000418093.2	n.437+8083T>G		intron_variant	Intron 4 of 4	4
ENSG00000273291	ENST00000443313.5	n.277+8083T>G		intron_variant	Intron 4 of 5	2		ENSP00000414848.1
ENSG00000273291	ENST00000451200.6	n.491+8083T>G		intron_variant	Intron 5 of 5	4

Frequencies

GnomAD3 genomes AF: 0.950 AC: 144546 AN: 152148 Hom.: 68861 Cov.: 32

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.967

Gnomad ASJ AF: 0.992

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.984

Gnomad FIN AF: 0.982

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.980

Gnomad OTH AF: 0.960

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

GnomAD4 genome AF: 0.950 AC: 144649 AN: 152266 Hom.: 68906 Cov.: 32 AF XY: 0.952 AC XY: 70870 AN XY: 74454

African (AFR) AF: 0.871 AC: 36151 AN: 41512

American (AMR) AF: 0.967 AC: 14800 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.992 AC: 3443 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5173 AN: 5174

South Asian (SAS) AF: 0.985 AC: 4750 AN: 4822

European-Finnish (FIN) AF: 0.982 AC: 10430 AN: 10618

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.980 AC: 66672 AN: 68036

Other (OTH) AF: 0.960 AC: 2032 AN: 2116

Alfa AF: 0.953 Hom.: 9617

Bravo AF: 0.946

Asia WGS AF: 0.988 AC: 3434 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	5.6
DANN	Benign	0.78
PhyloP100		0.043

Splicing

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

Other links and lift over

dbSNP: rs704894; hg19: chr3-42991646;