rs1691053

Variant names:

• chr5-6677052-T-C
• rs1691053

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0358 AC: 1488 AN: 41576

American (AMR) AF: 0.183 AC: 2802 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0614 AC: 213 AN: 3468

East Asian (EAS) AF: 0.280 AC: 1448 AN: 5172

South Asian (SAS) AF: 0.161 AC: 776 AN: 4828

European-Finnish (FIN) AF: 0.155 AC: 1640 AN: 10600

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6817 AN: 68012

Other (OTH) AF: 0.0941 AC: 199 AN: 2114

Alfa AF: 0.112 Hom.: 539

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
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1691053; hg19: chr5-6677165;