rs1369977

Variant names:

• chr4-95887122-G-A
• rs1369977

Your query was ambiguous. Multiple possible variants found:

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

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 0.926 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
• Publications: 2 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 = 0.975 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: 0.927 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

African (AFR) AF: 0.924 AC: 38333 AN: 41472

American (AMR) AF: 0.934 AC: 14221 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3163 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5105 AN: 5116

South Asian (SAS) AF: 0.867 AC: 4179 AN: 4820

European-Finnish (FIN) AF: 0.971 AC: 10290 AN: 10598

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.918 AC: 62343 AN: 67876

Other (OTH) AF: 0.925 AC: 1953 AN: 2112

Alfa AF: 0.912 Hom.: 26505

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
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs1369977; hg19: chr4-96808273;