chr3-36368109-T-G

Variant names:

• chr3-36368109-T-G
• rs2605393
• ENST00000792147.1:n.331-33148A>C

Variant summary

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

The ENST00000792147.1(ENSG00000303138):​n.331-33148A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,962 control chromosomes in the GnomAD database, including 12,883 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 0.39 (12883 hom., cov: 32)
• Consequence: ENSG00000303138 ENST00000792147.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506
• Publications: 5 publications found

Genes affected

ENSG00000303138 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000792147.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303138	ENST00000792147.1		n.331-33148A>C		intron	N/A
	ENSG00000303138	ENST00000792148.1		n.142+12685A>C		intron	N/A
	ENSG00000303138	ENST00000792149.1		n.114+12685A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58635 AN: 151844 Hom.: 12849 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.386 AC: 58716 AN: 151962 Hom.: 12883 Cov.: 32 AF XY: 0.382 AC XY: 28364 AN XY: 74286

African (AFR) AF: 0.619 AC: 25615 AN: 41414

American (AMR) AF: 0.350 AC: 5354 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1001 AN: 3468

East Asian (EAS) AF: 0.303 AC: 1567 AN: 5166

South Asian (SAS) AF: 0.343 AC: 1650 AN: 4816

European-Finnish (FIN) AF: 0.258 AC: 2731 AN: 10574

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19687 AN: 67938

Other (OTH) AF: 0.376 AC: 792 AN: 2104

Alfa AF: 0.323 Hom.: 15271

Bravo AF: 0.403

Asia WGS AF: 0.329 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.59
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs2605393; hg19: chr3-36409601;