2-164970433-G-T

Variant names:

• chr2-164970433-G-T
• rs10184126
• ENST00000414885.2:n.1153+11073G>T

Variant summary

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

The ENST00000414885.2(ENSG00000236283):​n.1153+11073G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 151,992 control chromosomes in the GnomAD database, including 10,414 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 0.36 (10414 hom., cov: 32)
• Consequence: ENSG00000236283 ENST00000414885.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425
• Publications: 10 publications found

Genes affected

ENSG00000236283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414885.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000236283	ENST00000414885.2	TSL:5	n.1153+11073G>T		intron	N/A
	ENSG00000236283	ENST00000627211.2	TSL:5	n.706+9466G>T		intron	N/A
	ENSG00000236283	ENST00000629991.2	TSL:5	n.673+9466G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54612 AN: 151874 Hom.: 10405 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.359 AC: 54641 AN: 151992 Hom.: 10414 Cov.: 32 AF XY: 0.356 AC XY: 26420 AN XY: 74302

African (AFR) AF: 0.238 AC: 9847 AN: 41444

American (AMR) AF: 0.325 AC: 4961 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1394 AN: 3470

East Asian (EAS) AF: 0.324 AC: 1671 AN: 5162

South Asian (SAS) AF: 0.265 AC: 1279 AN: 4818

European-Finnish (FIN) AF: 0.385 AC: 4063 AN: 10560

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.444 AC: 30152 AN: 67944

Other (OTH) AF: 0.347 AC: 730 AN: 2106

Alfa AF: 0.403 Hom.: 24139

Bravo AF: 0.349

Asia WGS AF: 0.279 AC: 974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.51
DANN	Benign	0.74
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs10184126; hg19: chr2-165826943;