rs6427627

chr1-154386703-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 0.385 in 151,974 control chromosomes in the GnomAD database, including 11,410 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 0.38 (11410 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 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: 0.385 AC: 58413 AN: 151858 Hom.: 11389 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.385 AC: 58469 AN: 151974 Hom.: 11410 Cov.: 32 AF XY: 0.384 AC XY: 28507 AN XY: 74252

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.360

Alfa AF: 0.375 Hom.: 1653

Bravo AF: 0.379

Asia WGS AF: 0.299 AC: 1044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.1
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6427627; hg19: chr1-154359179;