rs4122198

Positions:

• chr6-29777816-T-C

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 0.0888 in 152,234 control chromosomes in the GnomAD database, including 808 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 0.089 (808 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.693

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0886 AC: 13480 AN: 152116 Hom.: 796 Cov.: 32

Gnomad AFR AF: 0.0661

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0951

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.0724

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0706

Gnomad OTH AF: 0.0917

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

GnomAD4 genome AF: 0.0888 AC: 13512 AN: 152234 Hom.: 808 Cov.: 32 AF XY: 0.0931 AC XY: 6933 AN XY: 74436

Gnomad4 AFR AF: 0.0663

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.0951

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.0724

Gnomad4 NFE AF: 0.0706

Gnomad4 OTH AF: 0.0997

Alfa AF: 0.0817 Hom.: 690

Bravo AF: 0.0888

Asia WGS AF: 0.286 AC: 993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.7
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4122198; hg19: chr6-29745593;