ENST00000803240.1:n.624A>G

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373791	XR_007087614.1	n.242+1162A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304419	ENST00000803240.1	n.624A>G		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000304419	ENST00000803235.1	n.103+15526A>G		intron_variant	Intron 1 of 1
ENSG00000304419	ENST00000803236.1	n.457+1162A>G		intron_variant	Intron 3 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs6434304; hg19: chr2-189833911;