chr2-1773378-A-G

Variant names:

• chr2-1773378-A-G
• rs6735179
• ENST00000756694.1:n.1449T>C

Variant summary

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

The ENST00000756694.1(ENSG00000298587):​n.1449T>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 0.351 in 152,176 control chromosomes in the GnomAD database, including 10,566 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 0.35 (10566 hom., cov: 34)
• Consequence: ENSG00000298587 ENST00000756694.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.808
• Publications: 16 publications found

Genes affected

ENSG00000298587 (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 (AFR) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298587	ENST00000756694.1	n.1449T>C		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000298587	ENST00000756695.1	n.254T>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000298587	ENST00000756696.1	n.142T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53375 AN: 152058 Hom.: 10543 Cov.: 34

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.351 AC: 53450 AN: 152176 Hom.: 10566 Cov.: 34 AF XY: 0.355 AC XY: 26440 AN XY: 74398

African (AFR) AF: 0.529 AC: 21960 AN: 41516

American (AMR) AF: 0.221 AC: 3388 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 773 AN: 3472

East Asian (EAS) AF: 0.520 AC: 2682 AN: 5156

South Asian (SAS) AF: 0.362 AC: 1746 AN: 4824

European-Finnish (FIN) AF: 0.348 AC: 3688 AN: 10584

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18239 AN: 68004

Other (OTH) AF: 0.318 AC: 673 AN: 2114

Alfa AF: 0.289 Hom.: 10810

Bravo AF: 0.348

Asia WGS AF: 0.415 AC: 1442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.071
DANN	Benign	0.29
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs6735179; hg19: chr2-1777150;