rs1370967

Variant names:

• chr5-111203694-G-A
• rs1370967

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.140 AC: 5828 AN: 41484

American (AMR) AF: 0.0716 AC: 1093 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0285 AC: 99 AN: 3470

East Asian (EAS) AF: 0.193 AC: 999 AN: 5166

South Asian (SAS) AF: 0.108 AC: 519 AN: 4820

European-Finnish (FIN) AF: 0.0524 AC: 555 AN: 10598

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0391 AC: 2661 AN: 67984

Other (OTH) AF: 0.0674 AC: 142 AN: 2108

Alfa AF: 0.0683 Hom.: 161

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
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1370967; hg19: chr5-110539392;