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. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.764 AC: 31401 AN: 41102

American (AMR) AF: 0.604 AC: 9103 AN: 15080

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1789 AN: 3450

East Asian (EAS) AF: 0.996 AC: 5132 AN: 5152

South Asian (SAS) AF: 0.674 AC: 3233 AN: 4800

European-Finnish (FIN) AF: 0.509 AC: 5134 AN: 10088

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29584 AN: 67136

Other (OTH) AF: 0.550 AC: 1140 AN: 2072

Alfa AF: 0.489 Hom.: 65893

Bravo AF: 0.596

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.69
DANN	Benign	0.14
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1423741; hg19: chr16-61317091;