rs12651295

Positions:

• chr4-68906217-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.159 in 152,116 control chromosomes in the GnomAD database, including 2,240 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 (2240 hom., cov: 32)
• Consequence: LOC101930041 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

Genes affected

LOC101930041 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101930041		n.68906217A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000272626	ENST00000608365.1	n.109+658T>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24181 AN: 151998 Hom.: 2232 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0900

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.159 AC: 24208 AN: 152116 Hom.: 2240 Cov.: 32 AF XY: 0.157 AC XY: 11646 AN XY: 74366

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.0900

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.164

Alfa AF: 0.133 Hom.: 952

Bravo AF: 0.165

Asia WGS AF: 0.153 AC: 533 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12651295; hg19: chr4-69771935;