6-144277848-G-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 0.494 in 152,042 control chromosomes in the GnomAD database, including 19,281 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 0.49 (19281 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 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: 0.494 AC: 75042 AN: 151924 Hom.: 19247 Cov.: 32

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.494 AC: 75134 AN: 152042 Hom.: 19281 Cov.: 32 AF XY: 0.490 AC XY: 36433 AN XY: 74314

Gnomad4 AFR AF: 0.625

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.494

Alfa AF: 0.321 Hom.: 813

Bravo AF: 0.508

Asia WGS AF: 0.553 AC: 1922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.1
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs612928; hg19: chr6-144598984;