1-115378734-T-C

Variant names:

• chr1-115378734-T-C
• rs7552722

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 0.696 in 152,062 control chromosomes in the GnomAD database, including 37,621 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 0.70 (37621 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.864
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105705 AN: 151944 Hom.: 37570 Cov.: 31

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.696 AC: 105810 AN: 152062 Hom.: 37621 Cov.: 31 AF XY: 0.696 AC XY: 51712 AN XY: 74318

African (AFR) AF: 0.831 AC: 34463 AN: 41496

American (AMR) AF: 0.757 AC: 11563 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2548 AN: 3472

East Asian (EAS) AF: 0.732 AC: 3780 AN: 5166

South Asian (SAS) AF: 0.759 AC: 3650 AN: 4806

European-Finnish (FIN) AF: 0.574 AC: 6057 AN: 10560

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.612 AC: 41595 AN: 67968

Other (OTH) AF: 0.705 AC: 1490 AN: 2114

Alfa AF: 0.646 Hom.: 140706

Bravo AF: 0.714

Asia WGS AF: 0.723 AC: 2512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.51
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs7552722; hg19: chr1-115921355;