rs1424032

Variant names:

• chr16-62933249-A-G
• rs1424032
• ENST00000734827.1:n.62-10469T>C

Variant summary

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

The ENST00000734827.1(ENSG00000260658):​n.62-10469T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 151,806 control chromosomes in the GnomAD database, including 2,191 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 0.16 (2191 hom., cov: 32)
• Consequence: ENSG00000260658 ENST00000734827.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59
• Publications: 5 publications found

Genes affected

ENSG00000260658 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000734827.1. 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
	ENSG00000260658	ENST00000734827.1		n.62-10469T>C		intron	N/A
	ENSG00000260658	ENST00000734828.1		n.176-10469T>C		intron	N/A
	ENSG00000260658	ENST00000734829.1		n.57-10469T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24331 AN: 151688 Hom.: 2185 Cov.: 32

Gnomad AFR AF: 0.0814

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.160 AC: 24348 AN: 151806 Hom.: 2191 Cov.: 32 AF XY: 0.162 AC XY: 12048 AN XY: 74182

African (AFR) AF: 0.0817 AC: 3392 AN: 41524

American (AMR) AF: 0.198 AC: 3013 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 616 AN: 3458

East Asian (EAS) AF: 0.189 AC: 970 AN: 5138

South Asian (SAS) AF: 0.143 AC: 689 AN: 4822

European-Finnish (FIN) AF: 0.179 AC: 1890 AN: 10582

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.194 AC: 13170 AN: 67746

Other (OTH) AF: 0.165 AC: 346 AN: 2102

Alfa AF: 0.184 Hom.: 10812

Bravo AF: 0.162

Asia WGS AF: 0.154 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	14
DANN	Benign	0.65
PhyloP100		1.6

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: rs1424032;

hg19: chr16-62967153;