rs6426749

Variant names:

• chr1-22384980-G-C
• rs6426749

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 68 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.269 AC: 11142 AN: 41440

American (AMR) AF: 0.144 AC: 2196 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 640 AN: 3470

East Asian (EAS) AF: 0.216 AC: 1116 AN: 5170

South Asian (SAS) AF: 0.218 AC: 1051 AN: 4822

European-Finnish (FIN) AF: 0.0780 AC: 825 AN: 10576

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11699 AN: 67980

Other (OTH) AF: 0.189 AC: 399 AN: 2112

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6426749; hg19: chr1-22711473;