rs6659944

chr1-168810231-G-Achr1-168810231-G-Cchr1-168810231-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 0.575 in 151,970 control chromosomes in the GnomAD database, including 28,035 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 0.58 (28035 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 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: 0.575 AC: 87267 AN: 151852 Hom.: 27971 Cov.: 31

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.575 AC: 87394 AN: 151970 Hom.: 28035 Cov.: 31 AF XY: 0.582 AC XY: 43252 AN XY: 74264

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.985

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.524

Alfa AF: 0.455 Hom.: 8008

Bravo AF: 0.591

Asia WGS AF: 0.804 AC: 2793 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6659944; hg19: chr1-168779469;