20-32762102-T-C

Position:

• chr20-32762102-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 0.533 in 151,490 control chromosomes in the GnomAD database, including 23,419 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.53 (23419 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.270

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP6: Variant 20-32762102-T-C is Benign according to our data. Variant chr20-32762102-T-C is described in ClinVar as [Benign]. Clinvar id is 1170166.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32762102T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80679 AN: 151372 Hom.: 23386 Cov.: 31

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.533 AC: 80764 AN: 151490 Hom.: 23419 Cov.: 31 AF XY: 0.540 AC XY: 39929 AN XY: 73992

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.471

Alfa AF: 0.453 Hom.: 3910

Bravo AF: 0.549

Asia WGS AF: 0.736 AC: 2556 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Centromeric instability of chromosomes 1,9 and 16 and immunodeficiency Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 19, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.8
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6087990; hg19: chr20-31349908; COSMIC: COSV60192969;