rs6660565

Variant names:

• chr1-171292054-G-A
• rs6660565

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 0.399 in 151,838 control chromosomes in the GnomAD database, including 14,804 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 0.40 (14804 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841

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 = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60478 AN: 151718 Hom.: 14755 Cov.: 31

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.399 AC: 60578 AN: 151838 Hom.: 14804 Cov.: 31 AF XY: 0.396 AC XY: 29357 AN XY: 74222

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.378

Alfa AF: 0.290 Hom.: 14768

Bravo AF: 0.418

Asia WGS AF: 0.331 AC: 1153 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	1.1
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6660565; hg19: chr1-171261193;