1-160660353-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.363 in 151,908 control chromosomes in the GnomAD database, including 10,232 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 0.36 (10232 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55054 AN: 151790 Hom.: 10217 Cov.: 31

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.363 AC: 55117 AN: 151908 Hom.: 10232 Cov.: 31 AF XY: 0.361 AC XY: 26814 AN XY: 74252

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.338

Alfa AF: 0.337 Hom.: 19247

Bravo AF: 0.372

Asia WGS AF: 0.327 AC: 1135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.6
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11265461; hg19: chr1-160630143;