1-242711583-T-C

Variant names:

• chr1-242711583-T-C
• rs6676375

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 0.152 in 152,154 control chromosomes in the GnomAD database, including 1,818 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 0.15 (1818 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23043 AN: 152036 Hom.: 1805 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.152 AC: 23087 AN: 152154 Hom.: 1818 Cov.: 32 AF XY: 0.155 AC XY: 11508 AN XY: 74368

African (AFR) AF: 0.135 AC: 5624 AN: 41522

American (AMR) AF: 0.226 AC: 3455 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3470

East Asian (EAS) AF: 0.116 AC: 600 AN: 5158

South Asian (SAS) AF: 0.176 AC: 847 AN: 4818

European-Finnish (FIN) AF: 0.189 AC: 2000 AN: 10578

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9755 AN: 68008

Other (OTH) AF: 0.137 AC: 290 AN: 2112

Alfa AF: 0.149 Hom.: 3972

Bravo AF: 0.155

Asia WGS AF: 0.180 AC: 625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.73
DANN	Benign	0.49
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs6676375; hg19: chr1-242874885;