rs6907909

Variant names:

• chr6-132569609-A-G
• rs6907909

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.382 in 152,030 control chromosomes in the GnomAD database, including 12,100 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 (12100 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.772 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: 0.382 AC: 57965 AN: 151912 Hom.: 12080 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.382 AC: 58020 AN: 152030 Hom.: 12100 Cov.: 32 AF XY: 0.383 AC XY: 28462 AN XY: 74304

African (AFR) AF: 0.469 AC: 19426 AN: 41460

American (AMR) AF: 0.335 AC: 5110 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1021 AN: 3466

East Asian (EAS) AF: 0.793 AC: 4096 AN: 5168

South Asian (SAS) AF: 0.423 AC: 2039 AN: 4820

European-Finnish (FIN) AF: 0.292 AC: 3079 AN: 10562

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.324 AC: 22046 AN: 67974

Other (OTH) AF: 0.390 AC: 823 AN: 2110

Alfa AF: 0.361 Hom.: 1625

Bravo AF: 0.392

Asia WGS AF: 0.624 AC: 2167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.34
DANN	Benign	0.51
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs6907909; hg19: chr6-132890748; COSMIC: COSV51583065;