rs2269648

chr1-169586812-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.3 in 152,074 control chromosomes in the GnomAD database, including 8,580 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.30 (8580 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0850

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 1-169586812-C-T is Benign according to our data. Variant chr1-169586812-C-T is described in ClinVar as [Benign]. Clinvar id is 1232860.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 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: 0.299 AC: 45501 AN: 151958 Hom.: 8561 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.300 AC: 45549 AN: 152074 Hom.: 8580 Cov.: 32 AF XY: 0.302 AC XY: 22465 AN XY: 74346

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.282

Alfa AF: 0.246 Hom.: 1838

Bravo AF: 0.313

Asia WGS AF: 0.445 AC: 1546 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	1.6
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2269648; hg19: chr1-169556050;