3-121427214-T-C

Variant names:

• chr3-121427214-T-C
• rs2169302
• ENST00000666486.1:n.810+3175A>G

Variant summary

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

The ENST00000666486.1(ENSG00000287022):​n.810+3175A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,186 control chromosomes in the GnomAD database, including 1,285 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 0.12 (1285 hom., cov: 32)
• Consequence: ENSG00000287022 ENST00000666486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 3 publications found

Genes affected

ENSG00000287022 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 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
ENSG00000287022	ENST00000666486.1	n.810+3175A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18853 AN: 152068 Hom.: 1284 Cov.: 32

Gnomad AFR AF: 0.0681

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.124 AC: 18852 AN: 152186 Hom.: 1285 Cov.: 32 AF XY: 0.128 AC XY: 9497 AN XY: 74404

African (AFR) AF: 0.0681 AC: 2827 AN: 41542

American (AMR) AF: 0.111 AC: 1691 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 574 AN: 3468

East Asian (EAS) AF: 0.163 AC: 844 AN: 5184

South Asian (SAS) AF: 0.234 AC: 1131 AN: 4826

European-Finnish (FIN) AF: 0.166 AC: 1758 AN: 10578

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9622 AN: 67984

Other (OTH) AF: 0.131 AC: 277 AN: 2112

Alfa AF: 0.134 Hom.: 3977

Bravo AF: 0.116

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.34
DANN	Benign	0.80
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs2169302; hg19: chr3-121146061;