19-39241861-T-C

Variant names:

• chr19-39241861-T-C
• rs8105790
• ENST00000735578.1:n.116-1375T>C

Variant summary

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

The ENST00000735578.1(ENSG00000296032):​n.116-1375T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 151,888 control chromosomes in the GnomAD database, including 3,215 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 0.20 (3215 hom., cov: 31)
• Consequence: ENSG00000296032 ENST00000735578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495
• Publications: 51 publications found

Genes affected

ENSG00000296032 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.269 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
ENSG00000296032	ENST00000735578.1	n.116-1375T>C		intron_variant	Intron 1 of 1
ENSG00000296032	ENST00000735579.1	n.90-1375T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30356 AN: 151772 Hom.: 3216 Cov.: 31

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.0648

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.200 AC: 30385 AN: 151888 Hom.: 3215 Cov.: 31 AF XY: 0.195 AC XY: 14499 AN XY: 74280

African (AFR) AF: 0.208 AC: 8600 AN: 41310

American (AMR) AF: 0.275 AC: 4200 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 741 AN: 3470

East Asian (EAS) AF: 0.0652 AC: 337 AN: 5170

South Asian (SAS) AF: 0.160 AC: 770 AN: 4820

European-Finnish (FIN) AF: 0.138 AC: 1458 AN: 10602

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13594 AN: 67956

Other (OTH) AF: 0.206 AC: 435 AN: 2110

Alfa AF: 0.203 Hom.: 4897

Bravo AF: 0.213

Asia WGS AF: 0.114 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.24
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs8105790; hg19: chr19-39732501;