rs1369977

Positions:

• chr4-95887122-G-A
• chr4-95887122-G-C

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 0.926 in 151,890 control chromosomes in the GnomAD database, including 65,239 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 0.93 (65239 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111

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 = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.927 AC: 140625 AN: 151772 Hom.: 65203 Cov.: 31

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.971

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.918

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.926 AC: 140716 AN: 151890 Hom.: 65239 Cov.: 31 AF XY: 0.928 AC XY: 68879 AN XY: 74234

Gnomad4 AFR AF: 0.924

Gnomad4 AMR AF: 0.934

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.867

Gnomad4 FIN AF: 0.971

Gnomad4 NFE AF: 0.918

Gnomad4 OTH AF: 0.925

Alfa AF: 0.912 Hom.: 22938

Bravo AF: 0.926

Asia WGS AF: 0.919 AC: 3166 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1369977; hg19: chr4-96808273;