rs9977018

Variant names:

• chr21-41616809-T-G
• rs9977018

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 0.239 in 152,020 control chromosomes in the GnomAD database, including 4,691 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 0.24 (4691 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 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: 0.239 AC: 36371 AN: 151902 Hom.: 4692 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0342

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.239 AC: 36376 AN: 152020 Hom.: 4691 Cov.: 33 AF XY: 0.239 AC XY: 17737 AN XY: 74290

African (AFR) AF: 0.194 AC: 8065 AN: 41474

American (AMR) AF: 0.191 AC: 2909 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 799 AN: 3470

East Asian (EAS) AF: 0.0337 AC: 174 AN: 5168

South Asian (SAS) AF: 0.218 AC: 1053 AN: 4820

European-Finnish (FIN) AF: 0.328 AC: 3464 AN: 10546

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19189 AN: 67962

Other (OTH) AF: 0.215 AC: 454 AN: 2110

Alfa AF: 0.260 Hom.: 13420

Bravo AF: 0.224

Asia WGS AF: 0.0970 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.70
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs9977018; hg19: chr21-43036969;