ENST00000737540.1:n.436-6178A>G

Variant names:

• chr2-210752170-A-G
• rs2216405
• ENST00000737540.1:n.436-6178A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000737540.1(ENSG00000296241):​n.436-6178A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,138 control chromosomes in the GnomAD database, including 2,125 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 0.15 (2125 hom., cov: 32)
• Consequence: ENSG00000296241 ENST00000737540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.531
• Publications: 31 publications found

Genes affected

ENSG00000296241 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737540.1. 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
	ENSG00000296241	ENST00000737540.1		n.436-6178A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22553 AN: 152020 Hom.: 2121 Cov.: 32

Gnomad AFR AF: 0.0335

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.148 AC: 22554 AN: 152138 Hom.: 2125 Cov.: 32 AF XY: 0.155 AC XY: 11501 AN XY: 74364

African (AFR) AF: 0.0334 AC: 1386 AN: 41536

American (AMR) AF: 0.200 AC: 3050 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 557 AN: 3468

East Asian (EAS) AF: 0.155 AC: 801 AN: 5166

South Asian (SAS) AF: 0.188 AC: 908 AN: 4826

European-Finnish (FIN) AF: 0.287 AC: 3031 AN: 10564

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12315 AN: 67980

Other (OTH) AF: 0.141 AC: 297 AN: 2112

Alfa AF: 0.166 Hom.: 6736

Bravo AF: 0.137

Asia WGS AF: 0.155 AC: 540 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	15
DANN	Benign	0.82
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs2216405; hg19: chr2-211616894;