chr2-231516534-A-C

Variant names:

• chr2-231516534-A-C
• rs6754952
• ENST00000750933.1:n.194+1500A>C

Variant summary

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

The ENST00000750933.1(ENSG00000297785):​n.194+1500A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,956 control chromosomes in the GnomAD database, including 25,023 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 0.57 (25023 hom., cov: 31)
• Consequence: ENSG00000297785 ENST00000750933.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308
• Publications: 16 publications found

Genes affected

ENSG00000297785 (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 = 0.728 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750933.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297785	ENST00000750933.1		n.194+1500A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86362 AN: 151838 Hom.: 24986 Cov.: 31

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.569 AC: 86439 AN: 151956 Hom.: 25023 Cov.: 31 AF XY: 0.573 AC XY: 42509 AN XY: 74240

African (AFR) AF: 0.489 AC: 20252 AN: 41430

American (AMR) AF: 0.621 AC: 9495 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2526 AN: 3468

East Asian (EAS) AF: 0.747 AC: 3842 AN: 5140

South Asian (SAS) AF: 0.699 AC: 3366 AN: 4816

European-Finnish (FIN) AF: 0.577 AC: 6077 AN: 10540

Middle Eastern (MID) AF: 0.637 AC: 186 AN: 292

European-Non Finnish (NFE) AF: 0.571 AC: 38841 AN: 67970

Other (OTH) AF: 0.608 AC: 1283 AN: 2110

Alfa AF: 0.581 Hom.: 83114

Bravo AF: 0.569

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.58
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs6754952; hg19: chr2-232381245;