6-85014445-T-A

Position:

• chr6-85014445-T-A

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 0.387 in 151,840 control chromosomes in the GnomAD database, including 11,979 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 0.39 (11979 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.313

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58725 AN: 151722 Hom.: 11966 Cov.: 31

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.308

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.387 AC: 58787 AN: 151840 Hom.: 11979 Cov.: 31 AF XY: 0.398 AC XY: 29546 AN XY: 74232

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.365

Alfa AF: 0.215 Hom.: 465

Bravo AF: 0.393

Asia WGS AF: 0.516 AC: 1792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6919160; hg19: chr6-85724163;