rs16842422

Variant names:

• chr1-198130860-A-G
• rs16842422
• ENST00000787312.1:n.208-20768A>G

Variant summary

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

The ENST00000787312.1(ENSG00000302490):​n.208-20768A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,240 control chromosomes in the GnomAD database, including 1,018 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 0.10 (1018 hom., cov: 32)
• Consequence: ENSG00000302490 ENST00000787312.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406
• Publications: 4 publications found

Genes affected

ENSG00000302490 (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 (EAS) allele frequency at 95% confidence interval = 0.21 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
ENSG00000302490	ENST00000787312.1	n.208-20768A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15518 AN: 152122 Hom.: 1015 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0530

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0914

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0616

Gnomad OTH AF: 0.0861

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

GnomAD4 genome AF: 0.102 AC: 15535 AN: 152240 Hom.: 1018 Cov.: 32 AF XY: 0.105 AC XY: 7789 AN XY: 74434

African (AFR) AF: 0.162 AC: 6713 AN: 41516

American (AMR) AF: 0.103 AC: 1578 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0530 AC: 184 AN: 3472

East Asian (EAS) AF: 0.220 AC: 1140 AN: 5176

South Asian (SAS) AF: 0.108 AC: 519 AN: 4822

European-Finnish (FIN) AF: 0.0914 AC: 970 AN: 10608

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0616 AC: 4193 AN: 68034

Other (OTH) AF: 0.0848 AC: 179 AN: 2112

Alfa AF: 0.0889 Hom.: 114

Bravo AF: 0.107

Asia WGS AF: 0.168 AC: 584 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	0.50
DANN	Benign	0.36
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs16842422; hg19: chr1-198099990;