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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446977.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000273291	ENST00000446977.2	TSL:4	c.277+8083T>G		intron	N/A	ENSP00000477043.1
	ENSG00000273291	ENST00000418093.2	TSL:4	n.437+8083T>G		intron	N/A
	ENSG00000273291	ENST00000443313.5	TSL:2	n.277+8083T>G		intron	N/A	ENSP00000414848.1

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 v4.9

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;