chr6-144967129-A-C

Position:

• chr6-144967129-A-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 0.261 in 151,972 control chromosomes in the GnomAD database, including 7,587 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 0.26 (7587 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 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: 0.260 AC: 39542 AN: 151854 Hom.: 7565 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.261 AC: 39613 AN: 151972 Hom.: 7587 Cov.: 32 AF XY: 0.267 AC XY: 19828 AN XY: 74298

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.263

Alfa AF: 0.148 Hom.: 4594

Bravo AF: 0.275

Asia WGS AF: 0.439 AC: 1529 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.90
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7760387; hg19: chr6-145288265;