chr2-112846151-T-G

Variant names:

• chr2-112846151-T-G
• rs10169916
• ENST00000762706.1:n.405-39107T>G

Variant summary

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

The ENST00000762706.1(ENSG00000299339):​n.405-39107T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 152,108 control chromosomes in the GnomAD database, including 27,434 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 0.59 (27434 hom., cov: 33)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 22 publications found

Genes affected

ENSG00000299339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762706.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299339	ENST00000762706.1		n.405-39107T>G		intron	N/A
	ENSG00000299339	ENST00000762707.1		n.500-39107T>G		intron	N/A
	ENSG00000299339	ENST00000762708.1		n.266-39107T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90298 AN: 151990 Hom.: 27416 Cov.: 33

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.594 AC: 90343 AN: 152108 Hom.: 27434 Cov.: 33 AF XY: 0.586 AC XY: 43548 AN XY: 74362

African (AFR) AF: 0.527 AC: 21872 AN: 41468

American (AMR) AF: 0.507 AC: 7743 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2262 AN: 3472

East Asian (EAS) AF: 0.525 AC: 2717 AN: 5180

South Asian (SAS) AF: 0.408 AC: 1968 AN: 4822

European-Finnish (FIN) AF: 0.596 AC: 6310 AN: 10588

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45346 AN: 67984

Other (OTH) AF: 0.595 AC: 1257 AN: 2112

Alfa AF: 0.635 Hom.: 49845

Bravo AF: 0.588

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	12
DANN	Benign	0.89
PhyloP100		0.074

Splicing

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

Other links and lift over

dbSNP: rs10169916; hg19: chr2-113603728;