rs436044

Variant names:

• chr16-64928745-C-T
• rs436044

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 0.947 in 152,218 control chromosomes in the GnomAD database, including 68,274 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 0.95 (68274 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.947 AC: 143972 AN: 152098 Hom.: 68222 Cov.: 32

Gnomad AFR AF: 0.981

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.949

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

GnomAD4 genome AF: 0.947 AC: 144083 AN: 152218 Hom.: 68274 Cov.: 32 AF XY: 0.946 AC XY: 70374 AN XY: 74420

Gnomad4 AFR AF: 0.981

Gnomad4 AMR AF: 0.916

Gnomad4 ASJ AF: 0.963

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.960

Gnomad4 FIN AF: 0.907

Gnomad4 NFE AF: 0.933

Gnomad4 OTH AF: 0.949

Alfa AF: 0.939 Hom.: 97681

Bravo AF: 0.949

Asia WGS AF: 0.976 AC: 3395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs436044; hg19: chr16-64962648;