rs1370967

Variant names:

• chr5-111203694-G-A
• rs1370967

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;