rs2437896

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000438963.2(ENSG00000229066):​n.782-4904T>C variant causes a intron, non coding transcript 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: ENST00000438963.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.760

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373752	XR_923596.2	n.79+3077T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000438963.2	n.782-4904T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000653625.1	n.947+3077T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.660

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.415

Alfa AF: 0.320 Hom.: 18117

Bravo AF: 0.433

Asia WGS AF: 0.551 AC: 1916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2437896; hg19: chr2-176322489;