1-105396365-T-C

Variant names:

• chr1-105396365-T-C
• rs7554840

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 0.917 in 152,250 control chromosomes in the GnomAD database, including 64,897 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 0.92 (64897 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.985 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: 0.918 AC: 139590 AN: 152132 Hom.: 64859 Cov.: 33

Gnomad AFR AF: 0.833

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.971

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.914

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

GnomAD4 genome AF: 0.917 AC: 139685 AN: 152250 Hom.: 64897 Cov.: 33 AF XY: 0.914 AC XY: 68043 AN XY: 74428

African (AFR) AF: 0.833 AC: 34591 AN: 41528

American (AMR) AF: 0.889 AC: 13588 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.971 AC: 3371 AN: 3472

East Asian (EAS) AF: 0.534 AC: 2750 AN: 5148

South Asian (SAS) AF: 0.868 AC: 4187 AN: 4826

European-Finnish (FIN) AF: 0.997 AC: 10598 AN: 10626

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.992 AC: 67468 AN: 68042

Other (OTH) AF: 0.916 AC: 1935 AN: 2112

Alfa AF: 0.952 Hom.: 15632

Bravo AF: 0.903

Asia WGS AF: 0.729 AC: 2537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.3
DANN	Benign	0.39
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs7554840; hg19: chr1-105938987;