rs310405

Variant names:

• chr6-81090645-G-A
• rs310405

Your query was ambiguous. Multiple possible variants found:

• chr6-81090645-G-A
• chr6-81090645-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 0.446 in 151,988 control chromosomes in the GnomAD database, including 16,297 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 0.45 (16297 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.549 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: 0.447 AC: 67860 AN: 151870 Hom.: 16296 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.446 AC: 67860 AN: 151988 Hom.: 16297 Cov.: 32 AF XY: 0.441 AC XY: 32714 AN XY: 74258

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.554

Gnomad4 OTH AF: 0.449

Alfa AF: 0.530 Hom.: 36637

Bravo AF: 0.440

Asia WGS AF: 0.320 AC: 1116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.61
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs310405; hg19: chr6-81800362;