rs3217936

Variant names:

• chr12-4305786-G-C
• rs3217936
• ENST00000674624.1:n.720+16796G>C

Variant summary

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

The ENST00000674624.1(ENSG00000285901):​n.720+16796G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 152,076 control chromosomes in the GnomAD database, including 11,678 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 0.38 (11678 hom., cov: 32)
• Consequence: ENSG00000285901 ENST00000674624.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 7 publications found

Genes affected

ENSG00000285901 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 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
ENSG00000285901	ENST00000674624.1	n.720+16796G>C		intron_variant	Intron 4 of 9			ENSP00000501898.1
ENSG00000285901	ENST00000648100.1	n.720+16796G>C		intron_variant	Intron 4 of 11			ENSP00000497536.1

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57274 AN: 151958 Hom.: 11666 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.377 AC: 57324 AN: 152076 Hom.: 11678 Cov.: 32 AF XY: 0.375 AC XY: 27848 AN XY: 74346

African (AFR) AF: 0.521 AC: 21608 AN: 41452

American (AMR) AF: 0.270 AC: 4130 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 971 AN: 3472

East Asian (EAS) AF: 0.486 AC: 2511 AN: 5164

South Asian (SAS) AF: 0.362 AC: 1750 AN: 4828

European-Finnish (FIN) AF: 0.332 AC: 3514 AN: 10578

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21860 AN: 67978

Other (OTH) AF: 0.352 AC: 743 AN: 2112

Alfa AF: 0.366 Hom.: 1312

Bravo AF: 0.373

Asia WGS AF: 0.465 AC: 1617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.62
DANN	Benign	0.70
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs3217936; hg19: chr12-4414952;