chr2-34868226-T-G

Position:

• chr2-34868226-T-G

Variant summary

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

The ENST00000453451.5(ENSG00000226994):​n.180+36734T>G 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 0.121 in 152,192 control chromosomes in the GnomAD database, including 1,119 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 0.12 (1119 hom., cov: 32)
• Consequence: ENST00000453451.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.73

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 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
	ENST00000453451.5	n.180+36734T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18468 AN: 152074 Hom.: 1117 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0923

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.121 AC: 18478 AN: 152192 Hom.: 1119 Cov.: 32 AF XY: 0.120 AC XY: 8900 AN XY: 74404

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.0922

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.119

Alfa AF: 0.123 Hom.: 2436

Bravo AF: 0.121

Asia WGS AF: 0.108 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	17
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7600259; hg19: chr2-35093293;