7-101123428-C-T

Variant names:

• chr7-101123428-C-T
• rs6465787

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 0.0757 in 151,822 control chromosomes in the GnomAD database, including 950 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 0.076 (950 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.419

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 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: 0.0755 AC: 11448 AN: 151704 Hom.: 945 Cov.: 31

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0409

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.0243

Gnomad SAS AF: 0.0156

Gnomad FIN AF: 0.0611

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0150

Gnomad OTH AF: 0.0605

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

GnomAD4 genome AF: 0.0757 AC: 11486 AN: 151822 Hom.: 950 Cov.: 31 AF XY: 0.0762 AC XY: 5659 AN XY: 74228

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.0408

Gnomad4 ASJ AF: 0.0213

Gnomad4 EAS AF: 0.0246

Gnomad4 SAS AF: 0.0152

Gnomad4 FIN AF: 0.0611

Gnomad4 NFE AF: 0.0150

Gnomad4 OTH AF: 0.0598

Alfa AF: 0.00705 Hom.: 0

Bravo AF: 0.0833

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6465787; hg19: chr7-100766709;