rs2437896

Variant names:

• chr2-175457761-T-C
• rs2437896
• ENST00000438963.2:n.782-4904T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-175457761-T-C
• chr2-175457761-T-G

Variant summary

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

The ENST00000438963.2(ENSG00000229066):​n.782-4904T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 152,110 control chromosomes in the GnomAD database, including 14,235 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 0.41 (14235 hom., cov: 32)
• Consequence: ENSG00000229066 ENST00000438963.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.760
• Publications: 5 publications found

Genes affected

ENSG00000229066 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438963.2. 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
	ENSG00000229066	ENST00000438963.2	TSL:3	n.782-4904T>C		intron	N/A
	ENSG00000229066	ENST00000653625.1		n.947+3077T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61948 AN: 151992 Hom.: 14208 Cov.: 32

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.408 AC: 62019 AN: 152110 Hom.: 14235 Cov.: 32 AF XY: 0.409 AC XY: 30374 AN XY: 74344

African (AFR) AF: 0.604 AC: 25045 AN: 41466

American (AMR) AF: 0.442 AC: 6758 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1244 AN: 3468

East Asian (EAS) AF: 0.660 AC: 3408 AN: 5160

South Asian (SAS) AF: 0.433 AC: 2085 AN: 4816

European-Finnish (FIN) AF: 0.220 AC: 2332 AN: 10604

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19693 AN: 67990

Other (OTH) AF: 0.415 AC: 876 AN: 2112

Alfa AF: 0.337 Hom.: 27648

Bravo AF: 0.433

Asia WGS AF: 0.551 AC: 1916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.28
PhyloP100		-0.76

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2437896;

hg19: chr2-176322489;