3-160609801-G-T

Variant names:

• chr3-160609801-G-T
• rs6797357
• ENST00000758082.1:n.148-12958G>T

Variant summary

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

The ENST00000758082.1(ENSG00000293192):​n.148-12958G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 152,066 control chromosomes in the GnomAD database, including 46,175 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 0.75 (46175 hom., cov: 31)
• Consequence: ENSG00000293192 ENST00000758082.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450
• Publications: 5 publications found

Genes affected

ENSG00000293192 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000758082.1. 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
	ENSG00000293192	ENST00000758082.1		n.148-12958G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114256 AN: 151948 Hom.: 46164 Cov.: 31

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.851

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.752 AC: 114296 AN: 152066 Hom.: 46175 Cov.: 31 AF XY: 0.758 AC XY: 56338 AN XY: 74360

African (AFR) AF: 0.423 AC: 17489 AN: 41390

American (AMR) AF: 0.874 AC: 13365 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2824 AN: 3468

East Asian (EAS) AF: 0.959 AC: 4952 AN: 5166

South Asian (SAS) AF: 0.852 AC: 4111 AN: 4824

European-Finnish (FIN) AF: 0.889 AC: 9426 AN: 10600

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.873 AC: 59382 AN: 68004

Other (OTH) AF: 0.785 AC: 1659 AN: 2114

Alfa AF: 0.839 Hom.: 76889

Bravo AF: 0.738

Asia WGS AF: 0.829 AC: 2883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.12
DANN	Benign	0.77
PhyloP100		-0.045

Splicing

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

Other links and lift over

dbSNP: rs6797357; hg19: chr3-160327589;