rs1605022

Variant names:

• chr14-86244355-T-G
• rs1605022

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 0.0371 in 152,190 control chromosomes in the GnomAD database, including 191 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 0.037 (191 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0839 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: 0.0371 AC: 5638 AN: 152072 Hom.: 191 Cov.: 32

Gnomad AFR AF: 0.0864

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0213

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.0227

Gnomad SAS AF: 0.0103

Gnomad FIN AF: 0.0459

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.0292

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

GnomAD4 genome AF: 0.0371 AC: 5642 AN: 152190 Hom.: 191 Cov.: 32 AF XY: 0.0373 AC XY: 2776 AN XY: 74408

Gnomad4 AFR AF: 0.0863

Gnomad4 AMR AF: 0.0213

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.0230

Gnomad4 SAS AF: 0.0104

Gnomad4 FIN AF: 0.0459

Gnomad4 NFE AF: 0.0141

Gnomad4 OTH AF: 0.0284

Alfa AF: 0.0280 Hom.: 15

Bravo AF: 0.0376

Asia WGS AF: 0.0160 AC: 57 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1605022; hg19: chr14-86710699;