rs748404

chr15-43267033-T-C

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 0.175 in 152,266 control chromosomes in the GnomAD database, including 2,735 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.18 (2735 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.51

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BP6: Variant 15-43267033-T-C is Benign according to our data. Variant chr15-43267033-T-C is described in ClinVar as [Benign]. Clinvar id is 1276897.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.258 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: 0.175 AC: 26692 AN: 152148 Hom.: 2735 Cov.: 33

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.0415

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.175 AC: 26690 AN: 152266 Hom.: 2735 Cov.: 33 AF XY: 0.175 AC XY: 13017 AN XY: 74450

Gnomad4 AFR AF: 0.0895

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.0412

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.192

Alfa AF: 0.222 Hom.: 5957

Bravo AF: 0.177

Asia WGS AF: 0.139 AC: 488 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

May 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
Cadd	Benign	16
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs748404; hg19: chr15-43559231;