rs4972755

Variant names:

• chr2-175375121-G-A
• rs4972755
• ENST00000438963.2:n.248-67327G>A

Variant summary

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

The ENST00000438963.2(ENSG00000229066):​n.248-67327G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,048 control chromosomes in the GnomAD database, including 9,345 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 0.32 (9345 hom., cov: 32)
• Consequence: ENSG00000229066 ENST00000438963.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.850
• Publications: 12 publications found

Genes affected

ENSG00000229066 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438963.2. 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
	ENSG00000229066	ENST00000438963.2	TSL:3	n.248-67327G>A		intron	N/A
	ENSG00000229066	ENST00000444567.1	TSL:3	n.449-79487G>A		intron	N/A
	ENSG00000229066	ENST00000653625.1		n.337-67327G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49042 AN: 151930 Hom.: 9316 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.323 AC: 49114 AN: 152048 Hom.: 9345 Cov.: 32 AF XY: 0.322 AC XY: 23900 AN XY: 74332

African (AFR) AF: 0.508 AC: 21042 AN: 41442

American (AMR) AF: 0.359 AC: 5488 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 873 AN: 3470

East Asian (EAS) AF: 0.496 AC: 2558 AN: 5162

South Asian (SAS) AF: 0.339 AC: 1635 AN: 4826

European-Finnish (FIN) AF: 0.136 AC: 1438 AN: 10570

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14901 AN: 67998

Other (OTH) AF: 0.320 AC: 674 AN: 2108

Alfa AF: 0.264 Hom.: 10459

Bravo AF: 0.347

Asia WGS AF: 0.430 AC: 1490 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.14
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs4972755; hg19: chr2-176239849;