6-31449414-A-G

Position:

• chr6-31449414-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 0.21 in 151,532 control chromosomes in the GnomAD database, including 4,306 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 0.21 (4306 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.301 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: 0.210 AC: 31830 AN: 151414 Hom.: 4305 Cov.: 30

Gnomad AFR AF: 0.0899

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.0284

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.210 AC: 31840 AN: 151532 Hom.: 4306 Cov.: 30 AF XY: 0.203 AC XY: 14997 AN XY: 74040

Gnomad4 AFR AF: 0.0899

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.0282

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.182

Alfa AF: 0.277 Hom.: 9088

Bravo AF: 0.197

Asia WGS AF: 0.0880 AC: 310 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.2
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: rs3128982; hg19: chr6-31417191;