rs8110447

Variant names:

• chr19-29839537-G-A
• rs8110447
• ENST00000657512.1:n.1344C>T

Variant summary

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

The ENST00000657512.1(ENSG00000286538):​n.1344C>T 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 0.507 in 152,068 control chromosomes in the GnomAD database, including 20,207 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 0.51 (20207 hom., cov: 32)
• Consequence: ENSG00000286538 ENST00000657512.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790
• Publications: 3 publications found

Genes affected

ENSG00000286538 (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 = 0.636 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
ENSG00000286538	ENST00000657512.1	n.1344C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000286538	ENST00000775414.1	n.653+679C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.507 AC: 77094 AN: 151952 Hom.: 20185 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.507 AC: 77150 AN: 152068 Hom.: 20207 Cov.: 32 AF XY: 0.506 AC XY: 37605 AN XY: 74326

African (AFR) AF: 0.643 AC: 26648 AN: 41470

American (AMR) AF: 0.488 AC: 7451 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1535 AN: 3470

East Asian (EAS) AF: 0.491 AC: 2539 AN: 5168

South Asian (SAS) AF: 0.471 AC: 2271 AN: 4818

European-Finnish (FIN) AF: 0.375 AC: 3966 AN: 10564

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 31019 AN: 67976

Other (OTH) AF: 0.510 AC: 1078 AN: 2114

Alfa AF: 0.467 Hom.: 15556

Bravo AF: 0.520

Asia WGS AF: 0.490 AC: 1704 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	1.6
DANN	Benign	0.67
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs8110447; hg19: chr19-30330444;