3-61297047-G-T

Variant names:

• chr3-61297047-G-T
• rs7615788
• ENST00000809925.1:n.52-1443G>T

Variant summary

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

The ENST00000809925.1(ENSG00000305269):​n.52-1443G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 152,170 control chromosomes in the GnomAD database, including 51,306 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 0.81 (51306 hom., cov: 32)
• Consequence: ENSG00000305269 ENST00000809925.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107
• Publications: 2 publications found

Genes affected

ENSG00000305269 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809925.1. 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
	ENSG00000305269	ENST00000809925.1		n.52-1443G>T		intron	N/A
	ENSG00000305269	ENST00000809926.1		n.55-14920G>T		intron	N/A
	ENSG00000305269	ENST00000809927.1		n.256-14920G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.809 AC: 123060 AN: 152052 Hom.: 51276 Cov.: 32

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.915

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.809 AC: 123142 AN: 152170 Hom.: 51306 Cov.: 32 AF XY: 0.810 AC XY: 60297 AN XY: 74418

African (AFR) AF: 0.593 AC: 24580 AN: 41472

American (AMR) AF: 0.782 AC: 11962 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2987 AN: 3470

East Asian (EAS) AF: 0.923 AC: 4770 AN: 5168

South Asian (SAS) AF: 0.844 AC: 4065 AN: 4814

European-Finnish (FIN) AF: 0.931 AC: 9890 AN: 10620

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.915 AC: 62206 AN: 68012

Other (OTH) AF: 0.814 AC: 1719 AN: 2112

Alfa AF: 0.886 Hom.: 26932

Bravo AF: 0.791

Asia WGS AF: 0.852 AC: 2965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	15
DANN	Benign	0.52
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs7615788; hg19: chr3-61282721;