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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785002.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229131	ENST00000785002.1		n.619-8985G>A		intron	N/A
	ENSG00000229131	ENST00000785003.1		n.616-8985G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16842314;

hg19: chr2-140218360;