chr2-34868226-T-G

Variant names:

• chr2-34868226-T-G
• rs7600259
• ENST00000453451.5:n.180+36734T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000453451.5(ENSG00000226994):​n.180+36734T>G variant causes a intron 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: ENSG00000226994 ENST00000453451.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.73
• Publications: 3 publications found

Genes affected

ENSG00000226994 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000453451.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226994	ENST00000453451.5	TSL:4	n.180+36734T>G		intron	N/A
	ENSG00000226994	ENST00000585391.6	TSL:5	n.115+36734T>G		intron	N/A
	ENSG00000226994	ENST00000586769.6	TSL:5	n.157+36734T>G		intron	N/A

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

African (AFR) AF: 0.132 AC: 5495 AN: 41536

American (AMR) AF: 0.0922 AC: 1409 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3466

East Asian (EAS) AF: 0.117 AC: 608 AN: 5178

South Asian (SAS) AF: 0.112 AC: 542 AN: 4830

European-Finnish (FIN) AF: 0.111 AC: 1174 AN: 10614

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8247 AN: 67978

Other (OTH) AF: 0.119 AC: 251 AN: 2110

Alfa AF: 0.122 Hom.: 5111

Bravo AF: 0.121

Asia WGS AF: 0.108 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	17
DANN	Benign	0.79
PhyloP100		2.7
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs7600259; hg19: chr2-35093293;