rs4853750

Variant names:

• chr2-190874558-G-A
• rs4853750
• ENST00000772372.1:n.76-3187C>T

Variant summary

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

The ENST00000772372.1(ENSG00000228509):​n.76-3187C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 150,890 control chromosomes in the GnomAD database, including 1,240 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 0.11 (1240 hom., cov: 29)
• Consequence: ENSG00000228509 ENST00000772372.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 1 publications found

Genes affected

ENSG00000228509 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772372.1. 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
	ENSG00000228509	ENST00000772372.1		n.76-3187C>T		intron	N/A
	ENSG00000228509	ENST00000772376.1		n.161+7355C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16063 AN: 150806 Hom.: 1231 Cov.: 29

Gnomad AFR AF: 0.0900

Gnomad AMI AF: 0.0451

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.0368

Gnomad MID AF: 0.183

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.107 AC: 16081 AN: 150890 Hom.: 1240 Cov.: 29 AF XY: 0.109 AC XY: 8047 AN XY: 73608

African (AFR) AF: 0.0899 AC: 3690 AN: 41032

American (AMR) AF: 0.263 AC: 3990 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3464

East Asian (EAS) AF: 0.190 AC: 979 AN: 5144

South Asian (SAS) AF: 0.196 AC: 936 AN: 4778

European-Finnish (FIN) AF: 0.0368 AC: 374 AN: 10152

Middle Eastern (MID) AF: 0.186 AC: 52 AN: 280

European-Non Finnish (NFE) AF: 0.0782 AC: 5305 AN: 67852

Other (OTH) AF: 0.115 AC: 242 AN: 2098

Alfa AF: 0.0907 Hom.: 119

Bravo AF: 0.123

Asia WGS AF: 0.160 AC: 558 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.7
DANN	Benign	0.77
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs4853750; hg19: chr2-191739284;