rs622110

chr11-85957120-G-A

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 0.276 in 150,382 control chromosomes in the GnomAD database, including 5,938 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 0.28 (5938 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 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: 0.276 AC: 41540 AN: 150282 Hom.: 5935 Cov.: 31

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.276 AC: 41565 AN: 150382 Hom.: 5938 Cov.: 31 AF XY: 0.273 AC XY: 20012 AN XY: 73412

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.271

Alfa AF: 0.282 Hom.: 591

Bravo AF: 0.281

Asia WGS AF: 0.183 AC: 639 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.0
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs622110; hg19: chr11-85668163;