rs1370967

Positions:

• chr5-111203694-G-A

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 0.0788 in 152,096 control chromosomes in the GnomAD database, including 666 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 0.079 (666 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535

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 (EAS) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

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: 0.0787 AC: 11960 AN: 151978 Hom.: 663 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0719

Gnomad ASJ AF: 0.0285

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0524

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0391

Gnomad OTH AF: 0.0662

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

GnomAD4 genome AF: 0.0788 AC: 11980 AN: 152096 Hom.: 666 Cov.: 32 AF XY: 0.0797 AC XY: 5923 AN XY: 74336

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.0716

Gnomad4 ASJ AF: 0.0285

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0524

Gnomad4 NFE AF: 0.0391

Gnomad4 OTH AF: 0.0674

Alfa AF: 0.0574 Hom.: 45

Bravo AF: 0.0807

Asia WGS AF: 0.151 AC: 523 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	1.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1370967; hg19: chr5-110539392;