2-122638301-C-T

Position:

• chr2-122638301-C-T

Variant summary

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

The ENST00000657880.1(ENSG00000286481):​n.773+105382C>T 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 0.412 in 151,780 control chromosomes in the GnomAD database, including 14,186 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 (14186 hom., cov: 31)
• Consequence: ENST00000657880.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000657880.1	n.773+105382C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62517 AN: 151662 Hom.: 14183 Cov.: 31

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.412 AC: 62528 AN: 151780 Hom.: 14186 Cov.: 31 AF XY: 0.410 AC XY: 30400 AN XY: 74120

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.420

Alfa AF: 0.485 Hom.: 17480

Bravo AF: 0.401

Asia WGS AF: 0.381 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.092
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13400652; hg19: chr2-123395877;