15-63042555-G-GGAGGGCC

Position:

• chr15-63042555-G-GGAGGGCC

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The variant allele was found at a frequency of 0.0102 in 408,560 control chromosomes in the GnomAD database, including 43 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.011 (26 hom., cov: 32)
  • Exomes 𝑓: 0.0096 (17 hom.)
• Consequence: Unknown
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.87

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 15-63042555-G-GGAGGGCC is Benign according to our data. Variant chr15-63042555-G-GGAGGGCC is described in ClinVar as [Likely_benign]. Clinvar id is 1220336.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 26 gene

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0111 AC: 1691 AN: 152080 Hom.: 26 Cov.: 32

Gnomad AFR AF: 0.00263

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.00301

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.0466

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0140

Gnomad OTH AF: 0.00907

GnomAD4 exome AF: 0.00958 AC: 2456 AN: 256372 Hom.: 17 AF XY: 0.00836 AC XY: 1174 AN XY: 140394

Gnomad4 AFR exome AF: 0.00135

Gnomad4 AMR exome AF: 0.00307

Gnomad4 ASJ exome AF: 0.00842

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000572

Gnomad4 FIN exome AF: 0.0296

Gnomad4 NFE exome AF: 0.0121

Gnomad4 OTH exome AF: 0.00960

GnomAD4 genome AF: 0.0111 AC: 1691 AN: 152188 Hom.: 26 Cov.: 32 AF XY: 0.0122 AC XY: 906 AN XY: 74418

Gnomad4 AFR AF: 0.00262

Gnomad4 AMR AF: 0.00301

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.0466

Gnomad4 NFE AF: 0.0140

Gnomad4 OTH AF: 0.00898

Alfa AF: 0.00428 Hom.: 1

Asia WGS AF: 0.00116 AC: 5 AN: 3472

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2018

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs879682441; hg19: chr15-63334754;