1-211518364-G-T

Variant names:

• chr1-211518364-G-T
• rs7553035

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 0.17 in 152,180 control chromosomes in the GnomAD database, including 3,564 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 0.17 (3564 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 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: 0.170 AC: 25837 AN: 152062 Hom.: 3557 Cov.: 33

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0574

Gnomad SAS AF: 0.0818

Gnomad FIN AF: 0.0757

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0873

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.170 AC: 25876 AN: 152180 Hom.: 3564 Cov.: 33 AF XY: 0.166 AC XY: 12348 AN XY: 74414

African (AFR) AF: 0.378 AC: 15686 AN: 41464

American (AMR) AF: 0.110 AC: 1691 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 502 AN: 3472

East Asian (EAS) AF: 0.0569 AC: 295 AN: 5184

South Asian (SAS) AF: 0.0823 AC: 397 AN: 4824

European-Finnish (FIN) AF: 0.0757 AC: 803 AN: 10606

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0873 AC: 5938 AN: 68004

Other (OTH) AF: 0.158 AC: 334 AN: 2116

Alfa AF: 0.172 Hom.: 1630

Bravo AF: 0.183

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.052
DANN	Benign	0.48
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7553035; hg19: chr1-211691706;