7-48654357-C-T

Variant names:

• chr7-48654357-C-T
• rs6965361

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 0.095 in 152,152 control chromosomes in the GnomAD database, including 896 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 0.095 (896 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.15).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.196 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: 0.0950 AC: 14439 AN: 152034 Hom.: 891 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.0582

Gnomad EAS AF: 0.0914

Gnomad SAS AF: 0.0779

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0625

Gnomad OTH AF: 0.0942

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

GnomAD4 genome AF: 0.0950 AC: 14457 AN: 152152 Hom.: 896 Cov.: 32 AF XY: 0.102 AC XY: 7570 AN XY: 74382

African (AFR) AF: 0.108 AC: 4468 AN: 41528

American (AMR) AF: 0.202 AC: 3081 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0582 AC: 202 AN: 3468

East Asian (EAS) AF: 0.0918 AC: 474 AN: 5162

South Asian (SAS) AF: 0.0776 AC: 374 AN: 4820

European-Finnish (FIN) AF: 0.129 AC: 1362 AN: 10590

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0625 AC: 4249 AN: 68002

Other (OTH) AF: 0.0932 AC: 197 AN: 2114

Alfa AF: 0.0600 Hom.: 119

Bravo AF: 0.102

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.083
DANN	Benign	0.75
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6965361; hg19: chr7-48693953;