rs1036475

chr5-30720171-A-Gchr5-30720171-A-T

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 0.946 in 152,072 control chromosomes in the GnomAD database, including 68,091 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 0.95 (68091 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.609

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 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: 0.946 AC: 143769 AN: 151954 Hom.: 68036 Cov.: 33

Gnomad AFR AF: 0.941

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.970

Gnomad ASJ AF: 0.936

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.975

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.943

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

GnomAD4 genome AF: 0.946 AC: 143883 AN: 152072 Hom.: 68091 Cov.: 33 AF XY: 0.947 AC XY: 70367 AN XY: 74324

Gnomad4 AFR AF: 0.941

Gnomad4 AMR AF: 0.970

Gnomad4 ASJ AF: 0.936

Gnomad4 EAS AF: 0.976

Gnomad4 SAS AF: 0.975

Gnomad4 FIN AF: 0.908

Gnomad4 NFE AF: 0.947

Gnomad4 OTH AF: 0.943

Alfa AF: 0.922 Hom.: 3522

Bravo AF: 0.951

Asia WGS AF: 0.970 AC: 3372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.6
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1036475; hg19: chr5-30720278;