6-31440227-T-C

Position:

• chr6-31440227-T-C

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 0.0334 in 151,922 control chromosomes in the GnomAD database, including 142 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 0.033 (142 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0739 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: 0.0333 AC: 5059 AN: 151804 Hom.: 137 Cov.: 31

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0280

Gnomad ASJ AF: 0.0338

Gnomad EAS AF: 0.0801

Gnomad SAS AF: 0.0264

Gnomad FIN AF: 0.0231

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0351

Gnomad OTH AF: 0.0398

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

GnomAD4 genome AF: 0.0334 AC: 5079 AN: 151922 Hom.: 142 Cov.: 31 AF XY: 0.0332 AC XY: 2467 AN XY: 74294

Gnomad4 AFR AF: 0.0303

Gnomad4 AMR AF: 0.0280

Gnomad4 ASJ AF: 0.0338

Gnomad4 EAS AF: 0.0803

Gnomad4 SAS AF: 0.0266

Gnomad4 FIN AF: 0.0231

Gnomad4 NFE AF: 0.0351

Gnomad4 OTH AF: 0.0465

Alfa AF: 0.0347 Hom.: 113

Bravo AF: 0.0331

Asia WGS AF: 0.0510 AC: 178 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6938674; hg19: chr6-31408004;