rs4251700

Variant names:

• chr17-35807672-T-G
• rs4251700

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0582 in 152,276 control chromosomes in the GnomAD database, including 438 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 0.058 (438 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.545

ACMG classification

Verdict is Benign. Variant got -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 = 0.13 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: 0.0581 AC: 8843 AN: 152158 Hom.: 436 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0261

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.0360

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0255

Gnomad OTH AF: 0.0425

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

GnomAD4 genome AF: 0.0582 AC: 8860 AN: 152276 Hom.: 438 Cov.: 32 AF XY: 0.0574 AC XY: 4274 AN XY: 74456

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.0260

Gnomad4 ASJ AF: 0.0141

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0141

Gnomad4 FIN AF: 0.0360

Gnomad4 NFE AF: 0.0255

Gnomad4 OTH AF: 0.0449

Alfa AF: 0.0429 Hom.: 26

Bravo AF: 0.0623

Asia WGS AF: 0.0520 AC: 182 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	11
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4251700; hg19: chr17-34134676;