rs9461407

Variant names:

• chr6-27777959-G-A
• rs9461407

Your query was ambiguous. Multiple possible variants found:

• chr6-27777959-G-A
• chr6-27777959-G-C
• chr6-27777959-G-T

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 0.305 in 136,340 control chromosomes in the GnomAD database, including 7,540 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 0.31 (7540 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.501 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: 0.305 AC: 41618 AN: 136320 Hom.: 7532 Cov.: 25

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.202

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.305 AC: 41645 AN: 136340 Hom.: 7540 Cov.: 25 AF XY: 0.301 AC XY: 19619 AN XY: 65106

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.283

Alfa AF: 0.209 Hom.: 807

Bravo AF: 0.327

Asia WGS AF: 0.204 AC: 680 AN: 3322

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	0.0020
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9461407; hg19: chr6-27745738; COSMIC: COSV68925849;