chr4-89851700-A-C

Variant names:

• chr4-89851700-A-C
• rs2736993
• ENST00000776860.1:n.209-10738T>G

Variant summary

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

The ENST00000776860.1(ENSG00000301182):​n.209-10738T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,130 control chromosomes in the GnomAD database, including 3,333 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 0.19 (3333 hom., cov: 31)
• Consequence: ENSG00000301182 ENST00000776860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• Publications: 4 publications found

Genes affected

ENSG00000301182 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776860.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301182	ENST00000776860.1		n.209-10738T>G		intron	N/A
	ENSG00000301182	ENST00000776861.1		n.183-10738T>G		intron	N/A
	ENSG00000301182	ENST00000776862.1		n.203+3224T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28368 AN: 152012 Hom.: 3331 Cov.: 31

Gnomad AFR AF: 0.0662

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.187 AC: 28383 AN: 152130 Hom.: 3333 Cov.: 31 AF XY: 0.184 AC XY: 13692 AN XY: 74346

African (AFR) AF: 0.0661 AC: 2746 AN: 41538

American (AMR) AF: 0.176 AC: 2697 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 714 AN: 3472

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5170

South Asian (SAS) AF: 0.123 AC: 593 AN: 4810

European-Finnish (FIN) AF: 0.244 AC: 2578 AN: 10578

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18243 AN: 67958

Other (OTH) AF: 0.206 AC: 434 AN: 2110

Alfa AF: 0.218 Hom.: 528

Bravo AF: 0.179

Asia WGS AF: 0.0610 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.3
DANN	Benign	0.78
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs2736993; hg19: chr4-90772851;