1-67306330-T-C

Variant names:

• chr1-67306330-T-C
• rs11576006

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 0.231 in 151,992 control chromosomes in the GnomAD database, including 4,197 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 0.23 (4197 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35106 AN: 151870 Hom.: 4179 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.0639

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.231 AC: 35157 AN: 151992 Hom.: 4197 Cov.: 32 AF XY: 0.225 AC XY: 16682 AN XY: 74288

African (AFR) AF: 0.248 AC: 10262 AN: 41462

American (AMR) AF: 0.220 AC: 3363 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1233 AN: 3468

East Asian (EAS) AF: 0.0635 AC: 329 AN: 5182

South Asian (SAS) AF: 0.183 AC: 880 AN: 4810

European-Finnish (FIN) AF: 0.149 AC: 1575 AN: 10562

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.247 AC: 16762 AN: 67918

Other (OTH) AF: 0.261 AC: 550 AN: 2110

Alfa AF: 0.224 Hom.: 486

Bravo AF: 0.239

Asia WGS AF: 0.168 AC: 587 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.67
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs11576006; hg19: chr1-67772013;