1-65733540-C-T

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 0.75 in 152,132 control chromosomes in the GnomAD database, including 42,798 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 0.75 (42798 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 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: 0.750 AC: 113988 AN: 152014 Hom.: 42765 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.750 AC: 114076 AN: 152132 Hom.: 42798 Cov.: 32 AF XY: 0.753 AC XY: 55963 AN XY: 74366

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.804

Gnomad4 ASJ AF: 0.754

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.766

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.739

Gnomad4 OTH AF: 0.773

Alfa AF: 0.741 Hom.: 21532

Bravo AF: 0.749

Asia WGS AF: 0.843 AC: 2930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.1
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5010905; hg19: chr1-66199223;