rs1691053

chr5-6677052-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.102 in 152,270 control chromosomes in the GnomAD database, including 1,079 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.10 (1079 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 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: 0.102 AC: 15510 AN: 152152 Hom.: 1079 Cov.: 33

Gnomad AFR AF: 0.0358

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.0614

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0966

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

GnomAD4 genome AF: 0.102 AC: 15509 AN: 152270 Hom.: 1079 Cov.: 33 AF XY: 0.108 AC XY: 8030 AN XY: 74460

Gnomad4 AFR AF: 0.0358

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.0614

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.0941

Alfa AF: 0.108 Hom.: 307

Bravo AF: 0.101

Asia WGS AF: 0.243 AC: 843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	6.4
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1691053; hg19: chr5-6677165;