chr16-65787896-A-G

Variant names:

• chr16-65787896-A-G
• rs67302

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 0.428 in 151,968 control chromosomes in the GnomAD database, including 15,770 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 (15770 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 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: 0.428 AC: 64998 AN: 151850 Hom.: 15757 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.428 AC: 65035 AN: 151968 Hom.: 15770 Cov.: 32 AF XY: 0.439 AC XY: 32591 AN XY: 74292

African (AFR) AF: 0.219 AC: 9076 AN: 41460

American (AMR) AF: 0.522 AC: 7965 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1879 AN: 3470

East Asian (EAS) AF: 0.922 AC: 4767 AN: 5168

South Asian (SAS) AF: 0.506 AC: 2433 AN: 4810

European-Finnish (FIN) AF: 0.588 AC: 6202 AN: 10546

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31354 AN: 67934

Other (OTH) AF: 0.448 AC: 943 AN: 2104

Alfa AF: 0.453 Hom.: 8953

Bravo AF: 0.417

Asia WGS AF: 0.658 AC: 2287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.8
DANN	Benign	0.53
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs67302; hg19: chr16-65821799;