rs1605685

Positions:

• chr5-35458373-T-C

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 0.0989 in 152,216 control chromosomes in the GnomAD database, including 963 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 0.099 (963 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0989 AC: 15042 AN: 152098 Hom.: 963 Cov.: 33

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.0993

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.0903

Gnomad FIN AF: 0.0883

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.0864

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

GnomAD4 genome AF: 0.0989 AC: 15060 AN: 152216 Hom.: 963 Cov.: 33 AF XY: 0.103 AC XY: 7636 AN XY: 74416

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.0991

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.0906

Gnomad4 FIN AF: 0.0883

Gnomad4 NFE AF: 0.0597

Gnomad4 OTH AF: 0.0851

Alfa AF: 0.0702 Hom.: 933

Bravo AF: 0.104

Asia WGS AF: 0.145 AC: 505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	16
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1605685; hg19: chr5-35458475;