rs3744941

chr18-63476820-T-Cchr18-63476820-T-G

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 0.703 in 151,842 control chromosomes in the GnomAD database, including 38,170 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.70 (38147 hom., cov: 33)
  • Exomes 𝑓: 0.67 (23 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.376

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BP6: Variant 18-63476820-T-C is Benign according to our data. Variant chr18-63476820-T-C is described in ClinVar as [Benign]. Clinvar id is 1237193.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.839 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: 0.703 AC: 106523 AN: 151624 Hom.: 38097 Cov.: 33

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.689

GnomAD4 exome AF: 0.670 AC: 67 AN: 100 Hom.: 23 Cov.: 0 AF XY: 0.659 AC XY: 54 AN XY: 82

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.600

Gnomad4 NFE exome AF: 0.712

Gnomad4 OTH exome AF: 0.375

GnomAD4 genome AF: 0.703 AC: 106631 AN: 151742 Hom.: 38147 Cov.: 33 AF XY: 0.696 AC XY: 51594 AN XY: 74142

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.692

Alfa AF: 0.443 Hom.: 500

Bravo AF: 0.709

Asia WGS AF: 0.663 AC: 2306 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

Jan 29, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
Cadd	Benign	10
Dann	Benign	0.77

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3744941; hg19: chr18-61144053; COSMIC: COSV66976207; COSMIC: COSV66976207;