chr7-48755314-C-T

Variant names:

• chr7-48755314-C-T
• rs7801597

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 0.423 in 152,052 control chromosomes in the GnomAD database, including 13,906 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 0.42 (13906 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• 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 (EAS) allele frequency at 95% confidence interval = 0.576 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: 0.423 AC: 64264 AN: 151934 Hom.: 13907 Cov.: 33

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.423 AC: 64281 AN: 152052 Hom.: 13906 Cov.: 33 AF XY: 0.429 AC XY: 31859 AN XY: 74296

African (AFR) AF: 0.351 AC: 14567 AN: 41494

American (AMR) AF: 0.420 AC: 6423 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1475 AN: 3470

East Asian (EAS) AF: 0.593 AC: 3053 AN: 5148

South Asian (SAS) AF: 0.463 AC: 2227 AN: 4812

European-Finnish (FIN) AF: 0.480 AC: 5064 AN: 10548

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30128 AN: 67976

Other (OTH) AF: 0.424 AC: 897 AN: 2114

Alfa AF: 0.426 Hom.: 10002

Bravo AF: 0.413

Asia WGS AF: 0.471 AC: 1636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.18
DANN	Benign	0.64
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs7801597; hg19: chr7-48794910;