rs2646012

Variant names:

• chr4-99386631-G-C
• rs2646012
• ENST00000762194.1:n.378-3011C>G

Variant summary

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

The ENST00000762194.1(ENSG00000299279):​n.378-3011C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.886 in 152,174 control chromosomes in the GnomAD database, including 59,977 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 0.89 (59977 hom., cov: 31)
• Consequence: ENSG00000299279 ENST00000762194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 2 publications found

Genes affected

ENSG00000299279 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762194.1. 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
	ENSG00000299279	ENST00000762194.1		n.378-3011C>G		intron	N/A
	ENSG00000299279	ENST00000762195.1		n.250-3011C>G		intron	N/A
	ENSG00000299279	ENST00000762196.1		n.493-3011C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.886 AC: 134746 AN: 152056 Hom.: 59928 Cov.: 31

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.934

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.886 AC: 134856 AN: 152174 Hom.: 59977 Cov.: 31 AF XY: 0.885 AC XY: 65842 AN XY: 74386

African (AFR) AF: 0.937 AC: 38911 AN: 41544

American (AMR) AF: 0.829 AC: 12659 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2620 AN: 3470

East Asian (EAS) AF: 0.856 AC: 4426 AN: 5172

South Asian (SAS) AF: 0.934 AC: 4503 AN: 4820

European-Finnish (FIN) AF: 0.855 AC: 9049 AN: 10588

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59856 AN: 68002

Other (OTH) AF: 0.850 AC: 1791 AN: 2108

Alfa AF: 0.889 Hom.: 7498

Bravo AF: 0.882

Asia WGS AF: 0.833 AC: 2898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.40
PhyloP100		-0.54

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: rs2646012;

hg19: chr4-100307788;