2-56136242-T-C

Position:

• chr2-56136242-T-C

Variant summary

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

The ENST00000606639.1(ENSG00000272180):​n.160-11388T>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 0.389 in 152,006 control chromosomes in the GnomAD database, including 12,145 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 0.39 (12145 hom., cov: 31)
• Consequence: ENST00000606639.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374690	XR_940109.3	n.779-11388T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000606639.1	n.160-11388T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59097 AN: 151888 Hom.: 12136 Cov.: 31

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.389 AC: 59145 AN: 152006 Hom.: 12145 Cov.: 31 AF XY: 0.391 AC XY: 29022 AN XY: 74294

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.384

Alfa AF: 0.425 Hom.: 30468

Bravo AF: 0.395

Asia WGS AF: 0.360 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6751715; hg19: chr2-56363377;