rs6662889

Variant names:

• chr1-100809556-A-G
• rs6662889

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 0.361 in 151,890 control chromosomes in the GnomAD database, including 10,671 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 0.36 (10671 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.46 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: 0.361 AC: 54821 AN: 151772 Hom.: 10670 Cov.: 31

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.361 AC: 54838 AN: 151890 Hom.: 10671 Cov.: 31 AF XY: 0.360 AC XY: 26735 AN XY: 74196

African (AFR) AF: 0.222 AC: 9210 AN: 41442

American (AMR) AF: 0.351 AC: 5356 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1571 AN: 3472

East Asian (EAS) AF: 0.303 AC: 1563 AN: 5152

South Asian (SAS) AF: 0.476 AC: 2289 AN: 4810

European-Finnish (FIN) AF: 0.377 AC: 3981 AN: 10546

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29491 AN: 67910

Other (OTH) AF: 0.357 AC: 751 AN: 2104

Alfa AF: 0.382 Hom.: 1972

Bravo AF: 0.347

Asia WGS AF: 0.353 AC: 1225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.7
DANN	Benign	0.32
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs6662889; hg19: chr1-101275112; COSMIC: COSV69019912;