chr19-35290413-A-G

Variant names:

• chr19-35290413-A-G
• rs17705188
• ENST00000827558.1:n.391+2669T>C

Variant summary

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

The ENST00000827558.1(ENSG00000307628):​n.391+2669T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0447 in 152,220 control chromosomes in the GnomAD database, including 195 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 0.045 (195 hom., cov: 32)
• Consequence: ENSG00000307628 ENST00000827558.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 4 publications found

Genes affected

ENSG00000307628 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0708 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
ENSG00000307628	ENST00000827558.1	n.391+2669T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0446 AC: 6789 AN: 152102 Hom.: 193 Cov.: 32

Gnomad AFR AF: 0.0107

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.0628

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0772

Gnomad FIN AF: 0.0360

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.0621

Gnomad OTH AF: 0.0557

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

GnomAD4 genome AF: 0.0447 AC: 6799 AN: 152220 Hom.: 195 Cov.: 32 AF XY: 0.0437 AC XY: 3252 AN XY: 74422

African (AFR) AF: 0.0107 AC: 443 AN: 41548

American (AMR) AF: 0.0631 AC: 965 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0591 AC: 205 AN: 3468

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5180

South Asian (SAS) AF: 0.0773 AC: 373 AN: 4826

European-Finnish (FIN) AF: 0.0360 AC: 382 AN: 10612

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0621 AC: 4223 AN: 67994

Other (OTH) AF: 0.0551 AC: 116 AN: 2106

Alfa AF: 0.0621 Hom.: 392

Bravo AF: 0.0467

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.3
DANN	Benign	0.32
PhyloP100		-0.0050

Splicing

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

Other links and lift over

dbSNP: rs17705188; hg19: chr19-35781316;