rs696367

Variant names:

• chr3-108036107-C-G
• rs696367
• ENST00000652445.1:n.1416G>C

Your query was ambiguous. Multiple possible variants found:

• chr3-108036107-C-G
• chr3-108036107-C-T

Variant summary

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

The ENST00000652445.1(ENSG00000279277):​n.1416G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0764 in 152,156 control chromosomes in the GnomAD database, including 1,226 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 0.076 (1226 hom., cov: 32)
• Consequence: ENSG00000279277 ENST00000652445.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129
• Publications: 3 publications found

Genes affected

ENSG00000279277 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652445.1. 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
	ENSG00000279277	ENST00000652445.1		n.1416G>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000279277	ENST00000651058.1		n.1802+1284G>C		intron	N/A
	ENSG00000279277	ENST00000849536.1		n.23-1879G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0762 AC: 11588 AN: 152038 Hom.: 1219 Cov.: 32

Gnomad AFR AF: 0.0815

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0329

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.0602

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0204

Gnomad OTH AF: 0.0819

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

GnomAD4 genome AF: 0.0764 AC: 11618 AN: 152156 Hom.: 1226 Cov.: 32 AF XY: 0.0854 AC XY: 6350 AN XY: 74380

African (AFR) AF: 0.0814 AC: 3381 AN: 41514

American (AMR) AF: 0.145 AC: 2216 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0329 AC: 114 AN: 3468

East Asian (EAS) AF: 0.527 AC: 2713 AN: 5152

South Asian (SAS) AF: 0.203 AC: 976 AN: 4818

European-Finnish (FIN) AF: 0.0602 AC: 638 AN: 10594

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0204 AC: 1390 AN: 68006

Other (OTH) AF: 0.0853 AC: 180 AN: 2110

Alfa AF: 0.0121 Hom.: 6

Bravo AF: 0.0824

Asia WGS AF: 0.333 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	5.3
DANN	Benign	0.74
PhyloP100		0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs696367;

hg19: chr3-107754954;