rs6001118

chr22-38401013-T-Achr22-38401013-T-G

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 0.0509 in 152,248 control chromosomes in the GnomAD database, including 450 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 0.051 (450 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.666

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 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: 0.0509 AC: 7736 AN: 152130 Hom.: 445 Cov.: 32

Gnomad AFR AF: 0.0873

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.00662

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0237

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00872

Gnomad OTH AF: 0.0570

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

GnomAD4 genome AF: 0.0509 AC: 7756 AN: 152248 Hom.: 450 Cov.: 32 AF XY: 0.0529 AC XY: 3934 AN XY: 74436

Gnomad4 AFR AF: 0.0873

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.00662

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.0224

Gnomad4 FIN AF: 0.0237

Gnomad4 NFE AF: 0.00872

Gnomad4 OTH AF: 0.0631

Alfa AF: 0.0311 Hom.: 28

Bravo AF: 0.0609

Asia WGS AF: 0.112 AC: 390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	7.7
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6001118; hg19: chr22-38797018;