rs16933208

Variant names:

• chr12-5152277-A-C
• rs16933208
• ENST00000789688.1:n.278-17530A>C

Your query was ambiguous. Multiple possible variants found:

• chr12-5152277-A-C
• chr12-5152277-A-G
• chr12-5152277-A-T

Variant summary

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

The ENST00000789688.1(ENSG00000256417):​n.278-17530A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0187 in 152,292 control chromosomes in the GnomAD database, including 59 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 0.019 (59 hom., cov: 32)
• Consequence: ENSG00000256417 ENST00000789688.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• Publications: 1 publications found

Genes affected

ENSG00000256417 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369617	NR_188065.1	n.539-8030A>C		intron_variant	Intron 1 of 10
LOC105369617	NR_188066.1	n.522-8030A>C		intron_variant	Intron 1 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000256417	ENST00000789688.1	n.278-17530A>C		intron_variant	Intron 2 of 8
ENSG00000256417	ENST00000789689.1	n.270-8030A>C		intron_variant	Intron 2 of 11
ENSG00000256417	ENST00000789690.1	n.256-8030A>C		intron_variant	Intron 2 of 9

Frequencies

GnomAD3 genomes AF: 0.0187 AC: 2840 AN: 152174 Hom.: 59 Cov.: 32

Gnomad AFR AF: 0.0248

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.0583

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.0195

Gnomad SAS AF: 0.0327

Gnomad FIN AF: 0.00791

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00622

Gnomad OTH AF: 0.0267

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

GnomAD4 genome AF: 0.0187 AC: 2842 AN: 152292 Hom.: 59 Cov.: 32 AF XY: 0.0196 AC XY: 1459 AN XY: 74458

African (AFR) AF: 0.0247 AC: 1027 AN: 41552

American (AMR) AF: 0.0584 AC: 893 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0202 AC: 70 AN: 3472

East Asian (EAS) AF: 0.0193 AC: 100 AN: 5176

South Asian (SAS) AF: 0.0327 AC: 158 AN: 4826

European-Finnish (FIN) AF: 0.00791 AC: 84 AN: 10624

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00622 AC: 423 AN: 68030

Other (OTH) AF: 0.0265 AC: 56 AN: 2116

Alfa AF: 0.0186 Hom.: 15

Bravo AF: 0.0215

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.82
DANN	Benign	0.43
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs16933208; hg19: chr12-5261443;