rs1423946

Variant names:

• chr16-60102350-G-A
• rs1423946

Your query was ambiguous. Multiple possible variants found:

• chr16-60102350-G-A
• chr16-60102350-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.627 AC: 26011 AN: 41460

American (AMR) AF: 0.557 AC: 8491 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1601 AN: 3470

East Asian (EAS) AF: 0.665 AC: 3427 AN: 5152

South Asian (SAS) AF: 0.617 AC: 2969 AN: 4812

European-Finnish (FIN) AF: 0.570 AC: 6016 AN: 10560

Middle Eastern (MID) AF: 0.459 AC: 134 AN: 292

European-Non Finnish (NFE) AF: 0.524 AC: 35591 AN: 67948

Other (OTH) AF: 0.537 AC: 1136 AN: 2114

Alfa AF: 0.534 Hom.: 94884

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
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1423946; hg19: chr16-60136254;