rs1383972

Variant names:

• chr4-85463176-G-A
• rs1383972

Your query was ambiguous. Multiple possible variants found:

• chr4-85463176-G-A
• chr4-85463176-G-T

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 0.553 in 152,032 control chromosomes in the GnomAD database, including 26,310 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 0.55 (26310 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.391
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 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: 0.553 AC: 84082 AN: 151916 Hom.: 26297 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.553 AC: 84112 AN: 152032 Hom.: 26310 Cov.: 32 AF XY: 0.563 AC XY: 41849 AN XY: 74300

African (AFR) AF: 0.238 AC: 9889 AN: 41480

American (AMR) AF: 0.692 AC: 10570 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2100 AN: 3466

East Asian (EAS) AF: 0.810 AC: 4192 AN: 5178

South Asian (SAS) AF: 0.721 AC: 3474 AN: 4816

European-Finnish (FIN) AF: 0.716 AC: 7554 AN: 10546

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.651 AC: 44206 AN: 67950

Other (OTH) AF: 0.608 AC: 1285 AN: 2114

Alfa AF: 0.623 Hom.: 117698

Bravo AF: 0.538

Asia WGS AF: 0.743 AC: 2580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.54
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs1383972; hg19: chr4-86384329;