2-118049019-G-A

Position:

• chr2-118049019-G-A

Variant summary

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

The ENST00000627670.3(ENSG00000235066):​n.1227-5676G>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 0.285 in 151,980 control chromosomes in the GnomAD database, including 6,551 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 0.28 (6551 hom., cov: 32)
• Consequence: ENST00000627670.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723413	XR_427162.4	n.261-3568G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000627670.3	n.1227-5676G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000627626.1	n.247-5701G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43283 AN: 151864 Hom.: 6544 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.285 AC: 43313 AN: 151980 Hom.: 6551 Cov.: 32 AF XY: 0.281 AC XY: 20872 AN XY: 74320

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.269

Alfa AF: 0.270 Hom.: 967

Bravo AF: 0.287

Asia WGS AF: 0.220 AC: 765 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.9
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6746842; hg19: chr2-118806595;