3-110249952-G-T

Variant names:

• chr3-110249952-G-T
• rs7641787
• ENST00000779752.1:n.129+2489G>T

Variant summary

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

The ENST00000779752.1(ENSG00000301569):​n.129+2489G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 151,822 control chromosomes in the GnomAD database, including 5,327 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 0.22 (5327 hom., cov: 32)
• Consequence: ENSG00000301569 ENST00000779752.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 1 publications found

Genes affected

ENSG00000301569 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779752.1. 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
	ENSG00000301569	ENST00000779752.1		n.129+2489G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34032 AN: 151706 Hom.: 5306 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0859

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.225 AC: 34102 AN: 151822 Hom.: 5327 Cov.: 32 AF XY: 0.224 AC XY: 16599 AN XY: 74228

African (AFR) AF: 0.429 AC: 17762 AN: 41414

American (AMR) AF: 0.270 AC: 4117 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 661 AN: 3466

East Asian (EAS) AF: 0.266 AC: 1375 AN: 5160

South Asian (SAS) AF: 0.130 AC: 626 AN: 4820

European-Finnish (FIN) AF: 0.0859 AC: 910 AN: 10598

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8089 AN: 67826

Other (OTH) AF: 0.217 AC: 456 AN: 2098

Alfa AF: 0.178 Hom.: 1434

Bravo AF: 0.248

Asia WGS AF: 0.225 AC: 780 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.17
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs7641787; hg19: chr3-109968799;