rs4949316

Variant names:

• chr1-30842746-G-C
• rs4949316
• ENST00000752831.1:n.212C>G

Your query was ambiguous. Multiple possible variants found:

• chr1-30842746-G-C
• chr1-30842746-G-T

Variant summary

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

The ENST00000752831.1(ENSG00000298070):​n.212C>G 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 0.616 in 152,138 control chromosomes in the GnomAD database, including 30,694 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 0.62 (30694 hom., cov: 32)
• Consequence: ENSG00000298070 ENST00000752831.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.863
• Publications: 7 publications found

Genes affected

ENSG00000298070 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752831.1. 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
	ENSG00000298070	ENST00000752831.1		n.212C>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93706 AN: 152020 Hom.: 30680 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.616 AC: 93740 AN: 152138 Hom.: 30694 Cov.: 32 AF XY: 0.620 AC XY: 46078 AN XY: 74374

African (AFR) AF: 0.382 AC: 15849 AN: 41460

American (AMR) AF: 0.742 AC: 11356 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2254 AN: 3472

East Asian (EAS) AF: 0.704 AC: 3643 AN: 5178

South Asian (SAS) AF: 0.571 AC: 2755 AN: 4828

European-Finnish (FIN) AF: 0.733 AC: 7756 AN: 10584

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47829 AN: 68000

Other (OTH) AF: 0.638 AC: 1348 AN: 2114

Alfa AF: 0.565 Hom.: 1833

Bravo AF: 0.608

Asia WGS AF: 0.602 AC: 2092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.6
DANN	Benign	0.42
PhyloP100		0.86

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: rs4949316;

hg19: chr1-31315593;

COSMIC: COSV68497104;