rs6001118

Variant names:

• chr22-38401013-T-A
• rs6001118

Your query was ambiguous. Multiple possible variants found:

• chr22-38401013-T-A
• chr22-38401013-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;