rs6426749

Positions:

• chr1-22384980-G-C
• chr1-22384980-G-T

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 0.193 in 152,054 control chromosomes in the GnomAD database, including 3,106 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 0.19 (3106 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 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: 0.192 AC: 29242 AN: 151936 Hom.: 3099 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.0780

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.193 AC: 29280 AN: 152054 Hom.: 3106 Cov.: 32 AF XY: 0.187 AC XY: 13913 AN XY: 74330

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.0780

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.189

Alfa AF: 0.0807 Hom.: 94

Bravo AF: 0.201

Asia WGS AF: 0.216 AC: 752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.30
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6426749; hg19: chr1-22711473;