6-31384854-A-G

Position:

• chr6-31384854-A-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 0.36 in 151,468 control chromosomes in the GnomAD database, including 10,257 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 0.36 (10257 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54447 AN: 151346 Hom.: 10244 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.360 AC: 54505 AN: 151468 Hom.: 10257 Cov.: 32 AF XY: 0.366 AC XY: 27069 AN XY: 74052

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.393

Alfa AF: 0.338 Hom.: 6061

Bravo AF: 0.363

Asia WGS AF: 0.349 AC: 1216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7741091; hg19: chr6-31352631;