2-44253811-G-C

Variant names:

• chr2-44253811-G-C
• rs4953076
• ENST00000649044.1:n.1135-21693G>C

Variant summary

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

The ENST00000649044.1(ENSG00000285542):​n.1135-21693G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 151,978 control chromosomes in the GnomAD database, including 39,744 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 0.72 (39744 hom., cov: 32)
• Consequence: ENSG00000285542 ENST00000649044.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235

Genes affected

ENSG00000285542 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.807 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
ENSG00000285542	ENST00000649044.1	n.1135-21693G>C		intron_variant	Intron 5 of 14			ENSP00000497083.1

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109143 AN: 151862 Hom.: 39702 Cov.: 32

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.719 AC: 109241 AN: 151978 Hom.: 39744 Cov.: 32 AF XY: 0.714 AC XY: 52995 AN XY: 74272

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.829

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.727

Alfa AF: 0.656 Hom.: 1875

Bravo AF: 0.710

Asia WGS AF: 0.641 AC: 2235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.4
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4953076; hg19: chr2-44480950;