rs4786370

Variant names:

• chr16-3063897-T-C
• rs4786370

Your query was ambiguous. Multiple possible variants found:

• chr16-3063897-T-C
• chr16-3063897-T-G

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 0.425 in 151,962 control chromosomes in the GnomAD database, including 14,134 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 0.43 (14134 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 20 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 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: 0.425 AC: 64580 AN: 151844 Hom.: 14136 Cov.: 31

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.425 AC: 64599 AN: 151962 Hom.: 14134 Cov.: 31 AF XY: 0.431 AC XY: 32048 AN XY: 74286

African (AFR) AF: 0.391 AC: 16170 AN: 41394

American (AMR) AF: 0.436 AC: 6669 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1476 AN: 3470

East Asian (EAS) AF: 0.742 AC: 3837 AN: 5168

South Asian (SAS) AF: 0.534 AC: 2572 AN: 4816

European-Finnish (FIN) AF: 0.415 AC: 4376 AN: 10556

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 27997 AN: 67966

Other (OTH) AF: 0.453 AC: 956 AN: 2110

Alfa AF: 0.422 Hom.: 29417

Bravo AF: 0.425

Asia WGS AF: 0.620 AC: 2156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.75
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs4786370; hg19: chr16-3113898;