rs2736108

chr5-1297373-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 0.244 in 152,164 control chromosomes in the GnomAD database, including 5,188 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.24 (5188 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.679

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 5-1297373-C-T is Benign according to our data. Variant chr5-1297373-C-T is described in ClinVar as [Benign]. Clinvar id is 225785.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.499 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: 0.244 AC: 37151 AN: 152046 Hom.: 5179 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.244 AC: 37171 AN: 152164 Hom.: 5188 Cov.: 33 AF XY: 0.244 AC XY: 18187 AN XY: 74386

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.283

Alfa AF: 0.277 Hom.: 2550

Bravo AF: 0.236

Asia WGS AF: 0.412 AC: 1430 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Idiopathic Pulmonary Fibrosis;C3151443:Dyskeratosis congenita, autosomal dominant 2 Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 22, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.7
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2736108; hg19: chr5-1297488;