rs2360969

Positions:

• chr2-207508272-C-T

Variant summary

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

The ENST00000412387.5(ENSG00000223725):​n.260+9348G>A 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 0.313 in 152,036 control chromosomes in the GnomAD database, including 9,159 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 0.31 (9159 hom., cov: 32)
• Consequence: ENST00000412387.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000412387.5	n.260+9348G>A		intron_variant, non_coding_transcript_variant		4
	ENST00000418850.1	n.256+9348G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47556 AN: 151918 Hom.: 9158 Cov.: 32

Gnomad AFR AF: 0.0924

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.313 AC: 47561 AN: 152036 Hom.: 9159 Cov.: 32 AF XY: 0.313 AC XY: 23269 AN XY: 74316

Gnomad4 AFR AF: 0.0922

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.287

Alfa AF: 0.398 Hom.: 23292

Bravo AF: 0.297

Asia WGS AF: 0.233 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2360969; hg19: chr2-208372996;