chr3-106501867-T-C

Variant names:

• chr3-106501867-T-C
• rs2953040
• ENST00000668075.2:n.114-1054A>G

Variant summary

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

The ENST00000668075.2(ENSG00000291293):​n.114-1054A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 151,872 control chromosomes in the GnomAD database, including 22,156 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 0.54 (22156 hom., cov: 32)
• Consequence: ENSG00000291293 ENST00000668075.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• Publications: 2 publications found

Genes affected

ENSG00000291293 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668075.2. 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
	ENSG00000291293	ENST00000668075.2		n.114-1054A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81385 AN: 151752 Hom.: 22147 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.483

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.536 AC: 81435 AN: 151872 Hom.: 22156 Cov.: 32 AF XY: 0.539 AC XY: 39997 AN XY: 74224

African (AFR) AF: 0.464 AC: 19234 AN: 41454

American (AMR) AF: 0.598 AC: 9131 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2053 AN: 3470

East Asian (EAS) AF: 0.756 AC: 3912 AN: 5172

South Asian (SAS) AF: 0.613 AC: 2953 AN: 4820

European-Finnish (FIN) AF: 0.538 AC: 5649 AN: 10502

Middle Eastern (MID) AF: 0.493 AC: 137 AN: 278

European-Non Finnish (NFE) AF: 0.541 AC: 36746 AN: 67890

Other (OTH) AF: 0.551 AC: 1160 AN: 2106

Alfa AF: 0.537 Hom.: 3487

Bravo AF: 0.539

Asia WGS AF: 0.648 AC: 2230 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.8
DANN	Benign	0.87
PhyloP100		0.017

Splicing

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

Other links and lift over

dbSNP: rs2953040; hg19: chr3-106220714;