chr20-32762102-T-C

Variant names:

• chr20-32762102-T-C
• rs6087990

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.270
• Publications: 65 publications found

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.714 AC: 29566 AN: 41414

American (AMR) AF: 0.556 AC: 8472 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1501 AN: 3468

East Asian (EAS) AF: 0.924 AC: 4746 AN: 5136

South Asian (SAS) AF: 0.656 AC: 3149 AN: 4800

European-Finnish (FIN) AF: 0.432 AC: 4524 AN: 10472

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27290 AN: 67672

Other (OTH) AF: 0.471 AC: 989 AN: 2100

Alfa AF: 0.500 Hom.: 8936

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

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.8
DANN	Benign	0.86
PhyloP100		-0.27
PromoterAI		-0.0054	Neutral

Splicing

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

Other links and lift over

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