7-48654357-C-T

Variant names:

• chr7-48654357-C-T
• rs6965361

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.0582

Gnomad4 EAS AF: 0.0918

Gnomad4 SAS AF: 0.0776

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.0625

Gnomad4 OTH AF: 0.0932

Alfa AF: 0.0588 Hom.: 113

Bravo AF: 0.102

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6965361; hg19: chr7-48693953;