rs41309790

chr1-172658724-A-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 0.0974 in 152,304 control chromosomes in the GnomAD database, including 1,050 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.097 (1050 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.132

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 1-172658724-A-T is Benign according to our data. Variant chr1-172658724-A-T is described in ClinVar as [Benign]. Clinvar id is 1236304.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 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: 0.0975 AC: 14840 AN: 152186 Hom.: 1049 Cov.: 32

Gnomad AFR AF: 0.0245

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.0968

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0979

Gnomad FIN AF: 0.0818

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.0974 AC: 14841 AN: 152304 Hom.: 1050 Cov.: 32 AF XY: 0.0942 AC XY: 7016 AN XY: 74470

Gnomad4 AFR AF: 0.0245

Gnomad4 AMR AF: 0.0966

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0984

Gnomad4 FIN AF: 0.0818

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.114

Alfa AF: 0.113 Hom.: 132

Bravo AF: 0.0959

Asia WGS AF: 0.0420 AC: 148 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 08, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.3
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41309790; hg19: chr1-172627864;