rs6660565

Variant names:

• chr1-171292054-G-A
• rs6660565

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.701 AC: 28945 AN: 41300

American (AMR) AF: 0.359 AC: 5493 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 970 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1193 AN: 5166

South Asian (SAS) AF: 0.340 AC: 1638 AN: 4824

European-Finnish (FIN) AF: 0.260 AC: 2748 AN: 10560

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.274 AC: 18584 AN: 67926

Other (OTH) AF: 0.378 AC: 797 AN: 2108

Alfa AF: 0.309 Hom.: 25812

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
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs6660565; hg19: chr1-171261193;