rs9295740

Variant names:

• chr6-27721723-G-A
• rs9295740

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 0.261 in 151,962 control chromosomes in the GnomAD database, including 6,355 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 0.26 (6355 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.486

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 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: 0.261 AC: 39606 AN: 151844 Hom.: 6340 Cov.: 31

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.261 AC: 39664 AN: 151962 Hom.: 6355 Cov.: 31 AF XY: 0.256 AC XY: 19010 AN XY: 74292

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.252

Alfa AF: 0.194 Hom.: 6219

Bravo AF: 0.278

Asia WGS AF: 0.223 AC: 777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9295740; hg19: chr6-27689502;