chr6-7258384-C-T

Variant names:

• chr6-7258384-C-T
• rs9502570

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 0.375 in 152,148 control chromosomes in the GnomAD database, including 12,193 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 0.38 (12193 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 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: 0.375 AC: 56981 AN: 152030 Hom.: 12165 Cov.: 33

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.375 AC: 57071 AN: 152148 Hom.: 12193 Cov.: 33 AF XY: 0.377 AC XY: 28015 AN XY: 74402

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.316

Alfa AF: 0.308 Hom.: 4452

Bravo AF: 0.376

Asia WGS AF: 0.423 AC: 1473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.29
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9502570; hg19: chr6-7258617;