rs17428471

Variant names:

• chr7-27298248-G-T
• rs17428471

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 0.0927 in 140,616 control chromosomes in the GnomAD database, including 650 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 0.093 (650 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.742
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.119 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: 0.0927 AC: 13023 AN: 140544 Hom.: 648 Cov.: 29

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0869

Gnomad AMR AF: 0.0781

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0436

Gnomad SAS AF: 0.0439

Gnomad FIN AF: 0.0946

Gnomad MID AF: 0.0544

Gnomad NFE AF: 0.0835

Gnomad OTH AF: 0.0938

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

GnomAD4 genome AF: 0.0927 AC: 13036 AN: 140616 Hom.: 650 Cov.: 29 AF XY: 0.0922 AC XY: 6212 AN XY: 67400

African (AFR) AF: 0.122 AC: 4750 AN: 38926

American (AMR) AF: 0.0780 AC: 1054 AN: 13512

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 394 AN: 3368

East Asian (EAS) AF: 0.0435 AC: 197 AN: 4532

South Asian (SAS) AF: 0.0432 AC: 178 AN: 4116

European-Finnish (FIN) AF: 0.0946 AC: 715 AN: 7562

Middle Eastern (MID) AF: 0.0630 AC: 17 AN: 270

European-Non Finnish (NFE) AF: 0.0835 AC: 5469 AN: 65468

Other (OTH) AF: 0.0936 AC: 185 AN: 1976

Alfa AF: 0.0874 Hom.: 1031

Bravo AF: 0.0933

Asia WGS AF: 0.0350 AC: 121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.7
DANN	Benign	0.64
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs17428471; hg19: chr7-27337867;