16-65753982-T-G

Variant names:

• chr16-65753982-T-G
• rs1966963

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 0.436 in 152,010 control chromosomes in the GnomAD database, including 16,090 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 0.44 (16090 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 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: 0.436 AC: 66287 AN: 151894 Hom.: 16079 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.436 AC: 66325 AN: 152010 Hom.: 16090 Cov.: 32 AF XY: 0.446 AC XY: 33156 AN XY: 74308

African (AFR) AF: 0.223 AC: 9272 AN: 41490

American (AMR) AF: 0.534 AC: 8151 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1926 AN: 3472

East Asian (EAS) AF: 0.870 AC: 4491 AN: 5164

South Asian (SAS) AF: 0.502 AC: 2411 AN: 4806

European-Finnish (FIN) AF: 0.611 AC: 6447 AN: 10556

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32204 AN: 67930

Other (OTH) AF: 0.453 AC: 956 AN: 2112

Alfa AF: 0.451 Hom.: 11253

Bravo AF: 0.425

Asia WGS AF: 0.632 AC: 2197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.28
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1966963; hg19: chr16-65787885;