rs1423946

Positions:

• chr16-60102350-G-A
• chr16-60102350-G-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 0.565 in 151,972 control chromosomes in the GnomAD database, including 24,498 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 0.57 (24498 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85852 AN: 151852 Hom.: 24470 Cov.: 32

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.565 AC: 85925 AN: 151972 Hom.: 24498 Cov.: 32 AF XY: 0.567 AC XY: 42123 AN XY: 74258

Gnomad4 AFR AF: 0.627

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.617

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.537

Alfa AF: 0.528 Hom.: 44482

Bravo AF: 0.563

Asia WGS AF: 0.649 AC: 2258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.7
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1423946; hg19: chr16-60136254;