2-160925262-C-T

Variant names:

• chr2-160925262-C-T
• rs1722636
• ENST00000765752.1:n.109-4221G>A

Variant summary

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

The ENST00000765752.1(ENSG00000299704):​n.109-4221G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 151,966 control chromosomes in the GnomAD database, including 7,010 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 0.29 (7010 hom., cov: 32)
• Consequence: ENSG00000299704 ENST00000765752.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523
• Publications: 7 publications found

Genes affected

ENSG00000299704 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 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
ENSG00000299704	ENST00000765752.1	n.109-4221G>A		intron_variant	Intron 1 of 1
ENSG00000299704	ENST00000765753.1	n.136+3650G>A		intron_variant	Intron 2 of 2
ENSG00000299704	ENST00000765754.1	n.121+3650G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43625 AN: 151848 Hom.: 6976 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.288 AC: 43710 AN: 151966 Hom.: 7010 Cov.: 32 AF XY: 0.284 AC XY: 21133 AN XY: 74292

African (AFR) AF: 0.437 AC: 18107 AN: 41442

American (AMR) AF: 0.239 AC: 3649 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 945 AN: 3462

East Asian (EAS) AF: 0.186 AC: 958 AN: 5158

South Asian (SAS) AF: 0.288 AC: 1387 AN: 4812

European-Finnish (FIN) AF: 0.217 AC: 2287 AN: 10562

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15433 AN: 67962

Other (OTH) AF: 0.275 AC: 579 AN: 2106

Alfa AF: 0.243 Hom.: 13846

Bravo AF: 0.294

Asia WGS AF: 0.236 AC: 821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.7
DANN	Benign	0.72
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs1722636; hg19: chr2-161781773;