16-61498561-C-T

Variant names:

• chr16-61498561-C-T
• rs11075417

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 0.314 in 152,004 control chromosomes in the GnomAD database, including 8,255 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 0.31 (8255 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 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: 0.314 AC: 47669 AN: 151886 Hom.: 8247 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.314 AC: 47666 AN: 152004 Hom.: 8255 Cov.: 32 AF XY: 0.316 AC XY: 23483 AN XY: 74294

African (AFR) AF: 0.154 AC: 6404 AN: 41472

American (AMR) AF: 0.336 AC: 5125 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1595 AN: 3472

East Asian (EAS) AF: 0.522 AC: 2688 AN: 5148

South Asian (SAS) AF: 0.385 AC: 1858 AN: 4828

European-Finnish (FIN) AF: 0.341 AC: 3596 AN: 10544

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25267 AN: 67960

Other (OTH) AF: 0.347 AC: 733 AN: 2114

Alfa AF: 0.324 Hom.: 1357

Bravo AF: 0.308

Asia WGS AF: 0.385 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.23
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs11075417; hg19: chr16-61532465;