rs1502430

Variant names:

• chr16-77040450-A-G
• rs1502430
• ENST00000805261.1:n.306-14313T>C

Variant summary

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

The ENST00000805261.1(ENSG00000304662):​n.306-14313T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,118 control chromosomes in the GnomAD database, including 2,403 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 0.17 (2403 hom., cov: 33)
• Consequence: ENSG00000304662 ENST00000805261.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.878
• Publications: 1 publications found

Genes affected

ENSG00000304662 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.259 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
ENSG00000304662	ENST00000805261.1	n.306-14313T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25529 AN: 152000 Hom.: 2405 Cov.: 33

Gnomad AFR AF: 0.0794

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.168 AC: 25531 AN: 152118 Hom.: 2403 Cov.: 33 AF XY: 0.170 AC XY: 12642 AN XY: 74368

African (AFR) AF: 0.0794 AC: 3299 AN: 41534

American (AMR) AF: 0.160 AC: 2451 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 778 AN: 3470

East Asian (EAS) AF: 0.260 AC: 1337 AN: 5152

South Asian (SAS) AF: 0.271 AC: 1305 AN: 4818

European-Finnish (FIN) AF: 0.203 AC: 2154 AN: 10592

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13654 AN: 67950

Other (OTH) AF: 0.174 AC: 368 AN: 2110

Alfa AF: 0.177 Hom.: 318

Bravo AF: 0.161

Asia WGS AF: 0.234 AC: 811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.3
DANN	Benign	0.62
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs1502430; hg19: chr16-77074347;