rs16842314

Variant names:

• chr2-139460790-G-A
• rs16842314
• ENST00000785002.1:n.619-8985G>A

Variant summary

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

The ENST00000785002.1(ENSG00000229131):​n.619-8985G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0276 in 152,180 control chromosomes in the GnomAD database, including 145 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 0.028 (145 hom., cov: 32)
• Consequence: ENSG00000229131 ENST00000785002.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 1 publications found

Genes affected

ENSG00000229131 (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 = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373645	XR_007088681.1	n.616-8985G>A		intron_variant	Intron 1 of 1
LOC105373645	XR_923378.3	n.616-8985G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229131	ENST00000785002.1	n.619-8985G>A		intron_variant	Intron 1 of 2
ENSG00000229131	ENST00000785003.1	n.616-8985G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0276 AC: 4199 AN: 152062 Hom.: 142 Cov.: 32

Gnomad AFR AF: 0.00800

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0486

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.0523

Gnomad FIN AF: 0.0329

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.0215

Gnomad OTH AF: 0.0325

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

GnomAD4 genome AF: 0.0276 AC: 4199 AN: 152180 Hom.: 145 Cov.: 32 AF XY: 0.0303 AC XY: 2257 AN XY: 74380

African (AFR) AF: 0.00797 AC: 331 AN: 41518

American (AMR) AF: 0.0486 AC: 743 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 45 AN: 3470

East Asian (EAS) AF: 0.182 AC: 940 AN: 5178

South Asian (SAS) AF: 0.0513 AC: 247 AN: 4812

European-Finnish (FIN) AF: 0.0329 AC: 348 AN: 10586

Middle Eastern (MID) AF: 0.0103 AC: 3 AN: 292

European-Non Finnish (NFE) AF: 0.0214 AC: 1458 AN: 68000

Other (OTH) AF: 0.0355 AC: 75 AN: 2112

Alfa AF: 0.0223 Hom.: 83

Bravo AF: 0.0290

Asia WGS AF: 0.121 AC: 420 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	1.0
DANN	Benign	0.55
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs16842314; hg19: chr2-140218360;