rs1423741

Variant names:

• chr16-61283187-G-A
• rs1423741

Your query was ambiguous. Multiple possible variants found:

• chr16-61283187-G-A
• chr16-61283187-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 0.58 in 150,082 control chromosomes in the GnomAD database, including 27,094 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 0.58 (27094 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.311

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 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: 0.580 AC: 86931 AN: 149964 Hom.: 27040 Cov.: 28

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.580 AC: 87047 AN: 150082 Hom.: 27094 Cov.: 28 AF XY: 0.588 AC XY: 43151 AN XY: 73354

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.550

Alfa AF: 0.471 Hom.: 26748

Bravo AF: 0.596

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.69
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1423741; hg19: chr16-61317091;