16-61027486-T-C

Variant names:

• chr16-61027486-T-C
• rs1909766

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 0.233 in 148,120 control chromosomes in the GnomAD database, including 4,929 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 0.23 (4929 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240
• 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 (AFR) allele frequency at 95% confidence interval = 0.41 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: 0.233 AC: 34536 AN: 148060 Hom.: 4926 Cov.: 30

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.0863

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.0717

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.0967

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.233 AC: 34569 AN: 148120 Hom.: 4929 Cov.: 30 AF XY: 0.234 AC XY: 16853 AN XY: 72106

African (AFR) AF: 0.415 AC: 16855 AN: 40612

American (AMR) AF: 0.199 AC: 2939 AN: 14778

Ashkenazi Jewish (ASJ) AF: 0.0717 AC: 246 AN: 3432

East Asian (EAS) AF: 0.138 AC: 689 AN: 4992

South Asian (SAS) AF: 0.114 AC: 529 AN: 4640

European-Finnish (FIN) AF: 0.234 AC: 2250 AN: 9616

Middle Eastern (MID) AF: 0.0978 AC: 27 AN: 276

European-Non Finnish (NFE) AF: 0.158 AC: 10546 AN: 66808

Other (OTH) AF: 0.199 AC: 410 AN: 2062

Alfa AF: 0.141 Hom.: 936

Bravo AF: 0.236

Asia WGS AF: 0.138 AC: 479 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	4.0
DANN	Benign	0.47
PhyloP100		-0.024

Splicing

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

Other links and lift over

dbSNP: rs1909766; hg19: chr16-61061390;