6-144071249-G-T

Position:

• chr6-144071249-G-T

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 0.394 in 152,046 control chromosomes in the GnomAD database, including 12,764 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 (12764 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 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: 0.394 AC: 59897 AN: 151928 Hom.: 12748 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.394 AC: 59949 AN: 152046 Hom.: 12764 Cov.: 32 AF XY: 0.398 AC XY: 29597 AN XY: 74330

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.427

Alfa AF: 0.329 Hom.: 3682

Bravo AF: 0.412

Asia WGS AF: 0.318 AC: 1105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs763773; hg19: chr6-144392386; COSMIC: COSV60289821;