rs4972755

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000229066 (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 (AFR) allele frequency at 95% confidence interval = 0.502 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
ENSG00000229066	ENST00000438963.2	n.248-67327G>A		intron_variant	Intron 1 of 2	3
ENSG00000229066	ENST00000444567.1	n.449-79487G>A		intron_variant	Intron 2 of 2	3
ENSG00000229066	ENST00000653625.1	n.337-67327G>A		intron_variant	Intron 2 of 4

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

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.320

Alfa AF: 0.237 Hom.: 4985

Bravo AF: 0.347

Asia WGS AF: 0.430 AC: 1490 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4972755; hg19: chr2-176239849;