rs12650313

Positions:

• chr4-41705076-G-A
• chr4-41705076-G-T

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 0.155 in 152,148 control chromosomes in the GnomAD database, including 2,215 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 0.15 (2215 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23477 AN: 152030 Hom.: 2202 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0929

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.155 AC: 23534 AN: 152148 Hom.: 2215 Cov.: 32 AF XY: 0.158 AC XY: 11785 AN XY: 74382

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.0769

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.0929

Gnomad4 OTH AF: 0.120

Alfa AF: 0.102 Hom.: 1168

Bravo AF: 0.159

Asia WGS AF: 0.146 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.47
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12650313; hg19: chr4-41707093;