rs17207005

Positions:

• chr5-86143967-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0294 in 152,160 control chromosomes in the GnomAD database, including 84 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 0.029 (84 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0294 (4466/152160) while in subpopulation NFE AF= 0.0462 (3142/67984). AF 95% confidence interval is 0.0449. There are 84 homozygotes in gnomad4. There are 2067 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 84 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0294 AC: 4464 AN: 152044 Hom.: 83 Cov.: 31

Gnomad AFR AF: 0.00884

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0339

Gnomad ASJ AF: 0.0597

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00891

Gnomad FIN AF: 0.0106

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.0462

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0294 AC: 4466 AN: 152160 Hom.: 84 Cov.: 31 AF XY: 0.0278 AC XY: 2067 AN XY: 74394

Gnomad4 AFR AF: 0.00886

Gnomad4 AMR AF: 0.0339

Gnomad4 ASJ AF: 0.0597

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00891

Gnomad4 FIN AF: 0.0106

Gnomad4 NFE AF: 0.0462

Gnomad4 OTH AF: 0.0318

Alfa AF: 0.0323 Hom.: 13

Bravo AF: 0.0299

Asia WGS AF: 0.00549 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.43
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17207005; hg19: chr5-85439785;