2-210743655-T-G

Variant names:

• chr2-210743655-T-G
• rs4673553
• ENST00000737540.1:n.435+8056T>G

Variant summary

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

The ENST00000737540.1(ENSG00000296241):​n.435+8056T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 152,076 control chromosomes in the GnomAD database, including 14,623 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 0.42 (14623 hom., cov: 32)
• Consequence: ENSG00000296241 ENST00000737540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172
• Publications: 17 publications found

Genes affected

ENSG00000296241 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296241	ENST00000737540.1	n.435+8056T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63480 AN: 151958 Hom.: 14606 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.418 AC: 63531 AN: 152076 Hom.: 14623 Cov.: 32 AF XY: 0.426 AC XY: 31651 AN XY: 74342

African (AFR) AF: 0.239 AC: 9910 AN: 41512

American (AMR) AF: 0.479 AC: 7314 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1686 AN: 3466

East Asian (EAS) AF: 0.852 AC: 4407 AN: 5174

South Asian (SAS) AF: 0.458 AC: 2206 AN: 4816

European-Finnish (FIN) AF: 0.554 AC: 5857 AN: 10568

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30828 AN: 67944

Other (OTH) AF: 0.412 AC: 870 AN: 2114

Alfa AF: 0.433 Hom.: 22459

Bravo AF: 0.408

Asia WGS AF: 0.613 AC: 2129 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	1.9
DANN	Benign	0.82
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs4673553; hg19: chr2-211608379;