6-57257165-T-G

Position:

• chr6-57257165-T-G

Variant summary

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

The XM_047418987.1(PRIM2):​c.-10+35448T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,104 control chromosomes in the GnomAD database, including 5,977 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 0.24 (5977 hom., cov: 33)
• Consequence: PRIM2 XM_047418987.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564

Genes affected

PRIM2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRIM2	XM_047418987.1	c.-10+35448T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35770 AN: 151986 Hom.: 5961 Cov.: 33

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0321

Gnomad SAS AF: 0.0915

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.236 AC: 35828 AN: 152104 Hom.: 5977 Cov.: 33 AF XY: 0.227 AC XY: 16914 AN XY: 74386

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.0322

Gnomad4 SAS AF: 0.0920

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.194

Alfa AF: 0.236 Hom.: 821

Bravo AF: 0.246

Asia WGS AF: 0.0820 AC: 284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.65
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13213618; hg19: chr6-57121963;