rs16842502

Variant names:

• chr1-159684073-C-A
• rs16842502
• ENST00000751816.1:n.107+23384C>A

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.107+23384C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0575 in 152,246 control chromosomes in the GnomAD database, including 327 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 0.057 (327 hom., cov: 32)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.848
• Publications: 7 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751816.1. 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
	ENSG00000297913	ENST00000751816.1		n.107+23384C>A		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.109+23384C>A		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.62+23384C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0576 AC: 8761 AN: 152128 Hom.: 329 Cov.: 32

Gnomad AFR AF: 0.0301

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.0510

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0664

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.0598

Gnomad OTH AF: 0.0783

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

GnomAD4 genome AF: 0.0575 AC: 8751 AN: 152246 Hom.: 327 Cov.: 32 AF XY: 0.0585 AC XY: 4352 AN XY: 74450

African (AFR) AF: 0.0300 AC: 1245 AN: 41552

American (AMR) AF: 0.0510 AC: 780 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 397 AN: 3466

East Asian (EAS) AF: 0.157 AC: 812 AN: 5166

South Asian (SAS) AF: 0.105 AC: 504 AN: 4812

European-Finnish (FIN) AF: 0.0664 AC: 705 AN: 10614

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.0598 AC: 4067 AN: 68016

Other (OTH) AF: 0.0789 AC: 167 AN: 2116

Alfa AF: 0.0572 Hom.: 428

Bravo AF: 0.0541

Asia WGS AF: 0.0910 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.73
DANN	Benign	0.34
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs16842502; hg19: chr1-159653863;