2-10438981-T-C

Variant names:

• chr2-10438981-T-C
• rs28362433
• ENST00000757451.1:n.252-4701T>C

Variant summary

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

The ENST00000757451.1(ENSG00000298698):​n.252-4701T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0351 in 152,262 control chromosomes in the GnomAD database, including 512 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 0.035 (512 hom., cov: 32)
• Consequence: ENSG00000298698 ENST00000757451.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366
• Publications: 1 publications found

Genes affected

ENSG00000298698 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757451.1. 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
	ENSG00000298698	ENST00000757451.1		n.252-4701T>C		intron	N/A
	ENSG00000298698	ENST00000757452.1		n.133-2461T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0351 AC: 5339 AN: 152144 Hom.: 510 Cov.: 32

Gnomad AFR AF: 0.00529

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0477

Gnomad ASJ AF: 0.0276

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.0424

Gnomad FIN AF: 0.0908

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0145

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0351 AC: 5346 AN: 152262 Hom.: 512 Cov.: 32 AF XY: 0.0414 AC XY: 3083 AN XY: 74446

African (AFR) AF: 0.00527 AC: 219 AN: 41558

American (AMR) AF: 0.0484 AC: 740 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0276 AC: 96 AN: 3472

East Asian (EAS) AF: 0.402 AC: 2071 AN: 5148

South Asian (SAS) AF: 0.0418 AC: 202 AN: 4830

European-Finnish (FIN) AF: 0.0908 AC: 964 AN: 10620

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0145 AC: 989 AN: 68024

Other (OTH) AF: 0.0307 AC: 65 AN: 2114

Alfa AF: 0.0325 Hom.: 230

Bravo AF: 0.0344

Asia WGS AF: 0.191 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.36
DANN	Benign	0.64
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs28362433; hg19: chr2-10579107;