rs365188

Variant names:

• chr5-102741554-T-C
• rs365188
• ENST00000770037.1:n.1905A>G

Variant summary

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

The ENST00000770037.1(ENSG00000300209):​n.1905A>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 0.361 in 151,930 control chromosomes in the GnomAD database, including 10,392 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 0.36 (10392 hom., cov: 32)
• Consequence: ENSG00000300209 ENST00000770037.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• Publications: 5 publications found

Genes affected

ENSG00000300209 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 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
ENSG00000300209	ENST00000770037.1	n.1905A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000300209	ENST00000770034.1	n.383+14110A>G		intron_variant	Intron 1 of 1
ENSG00000300209	ENST00000770035.1	n.553+12966A>G		intron_variant	Intron 1 of 1
ENSG00000300209	ENST00000770036.1	n.444+12966A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54792 AN: 151812 Hom.: 10392 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.361 AC: 54813 AN: 151930 Hom.: 10392 Cov.: 32 AF XY: 0.364 AC XY: 26995 AN XY: 74258

African (AFR) AF: 0.252 AC: 10441 AN: 41480

American (AMR) AF: 0.370 AC: 5653 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 953 AN: 3464

East Asian (EAS) AF: 0.363 AC: 1870 AN: 5154

South Asian (SAS) AF: 0.413 AC: 1993 AN: 4822

European-Finnish (FIN) AF: 0.453 AC: 4765 AN: 10514

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27850 AN: 67898

Other (OTH) AF: 0.332 AC: 701 AN: 2114

Alfa AF: 0.383 Hom.: 1821

Bravo AF: 0.351

Asia WGS AF: 0.369 AC: 1276 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.60
PhyloP100		-0.084

Splicing

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

Other links and lift over

dbSNP: rs365188; hg19: chr5-102077258; COSMIC: COSV60174920;