rs11584656

Positions:

• chr1-17974230-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0109 in 152,266 control chromosomes in the GnomAD database, including 24 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 0.011 (24 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0109 (1656/152266) while in subpopulation NFE AF= 0.0163 (1105/67996). AF 95% confidence interval is 0.0155. There are 24 homozygotes in gnomad4. There are 843 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 24 gene

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: 0.0109 AC: 1659 AN: 152148 Hom.: 24 Cov.: 31

Gnomad AFR AF: 0.00220

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00432

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00746

Gnomad FIN AF: 0.0282

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0163

Gnomad OTH AF: 0.0110

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

GnomAD4 genome AF: 0.0109 AC: 1656 AN: 152266 Hom.: 24 Cov.: 31 AF XY: 0.0113 AC XY: 843 AN XY: 74446

Gnomad4 AFR AF: 0.00219

Gnomad4 AMR AF: 0.00431

Gnomad4 ASJ AF: 0.0104

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00705

Gnomad4 FIN AF: 0.0282

Gnomad4 NFE AF: 0.0163

Gnomad4 OTH AF: 0.0109

Alfa AF: 0.0153 Hom.: 2

Bravo AF: 0.00852

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.33
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11584656; hg19: chr1-18300724;