rs717177

Variant names:

• chr21-44739169-T-C
• rs717177

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 0.235 in 152,220 control chromosomes in the GnomAD database, including 5,017 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 0.23 (5017 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.4 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: 0.235 AC: 35703 AN: 152102 Hom.: 5015 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.235 AC: 35721 AN: 152220 Hom.: 5017 Cov.: 33 AF XY: 0.244 AC XY: 18174 AN XY: 74422

African (AFR) AF: 0.124 AC: 5170 AN: 41560

American (AMR) AF: 0.409 AC: 6250 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 668 AN: 3462

East Asian (EAS) AF: 0.347 AC: 1798 AN: 5182

South Asian (SAS) AF: 0.185 AC: 892 AN: 4826

European-Finnish (FIN) AF: 0.362 AC: 3832 AN: 10586

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16425 AN: 67994

Other (OTH) AF: 0.211 AC: 445 AN: 2112

Alfa AF: 0.241 Hom.: 15977

Bravo AF: 0.237

Asia WGS AF: 0.230 AC: 800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.4
DANN	Benign	0.67
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs717177; hg19: chr21-46159084;