rs9260378

Variant names:

• chr6-29950325-T-C
• rs9260378

Your query was ambiguous. Multiple possible variants found:

• chr6-29950325-T-C
• chr6-29950325-T-G

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 0.0821 in 143,758 control chromosomes in the GnomAD database, including 500 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 0.082 (500 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 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: 0.0820 AC: 11775 AN: 143652 Hom.: 494 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.0884

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.0156

Gnomad SAS AF: 0.0486

Gnomad FIN AF: 0.0481

Gnomad MID AF: 0.0777

Gnomad NFE AF: 0.0746

Gnomad OTH AF: 0.0953

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

GnomAD4 genome AF: 0.0821 AC: 11802 AN: 143758 Hom.: 500 Cov.: 32 AF XY: 0.0807 AC XY: 5688 AN XY: 70454

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.0883

Gnomad4 ASJ AF: 0.0813

Gnomad4 EAS AF: 0.0157

Gnomad4 SAS AF: 0.0487

Gnomad4 FIN AF: 0.0481

Gnomad4 NFE AF: 0.0746

Gnomad4 OTH AF: 0.0950

Alfa AF: 0.0225 Hom.: 9

Bravo AF: 0.0834

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.8
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9260378; hg19: chr6-29918102;