2-188969185-T-C

Variant names:

• chr2-188969185-T-C
• rs6434304
• ENST00000803240.1:n.624A>G

Variant summary

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

The ENST00000803240.1(ENSG00000304419):​n.624A>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 0.608 in 152,000 control chromosomes in the GnomAD database, including 28,664 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 0.61 (28664 hom., cov: 32)
• Consequence: ENSG00000304419 ENST00000803240.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 3 publications found

Genes affected

ENSG00000304419 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803240.1. 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
	ENSG00000304419	ENST00000803240.1		n.624A>G		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000304419	ENST00000803235.1		n.103+15526A>G		intron	N/A
	ENSG00000304419	ENST00000803236.1		n.457+1162A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92429 AN: 151880 Hom.: 28655 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.608 AC: 92476 AN: 152000 Hom.: 28664 Cov.: 32 AF XY: 0.612 AC XY: 45459 AN XY: 74318

African (AFR) AF: 0.477 AC: 19781 AN: 41444

American (AMR) AF: 0.612 AC: 9334 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1918 AN: 3468

East Asian (EAS) AF: 0.661 AC: 3419 AN: 5172

South Asian (SAS) AF: 0.657 AC: 3173 AN: 4830

European-Finnish (FIN) AF: 0.724 AC: 7663 AN: 10582

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45195 AN: 67940

Other (OTH) AF: 0.581 AC: 1223 AN: 2106

Alfa AF: 0.637 Hom.: 96793

Bravo AF: 0.592

Asia WGS AF: 0.673 AC: 2341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.44
PhyloP100		-1.1

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: rs6434304;

hg19: chr2-189833911;