rs1395093

Variant names:

• chr5-10018178-G-A
• rs1395093

Your query was ambiguous. Multiple possible variants found:

• chr5-10018178-G-A
• chr5-10018178-G-C
• chr5-10018178-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 0.574 in 151,968 control chromosomes in the GnomAD database, including 25,945 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 0.57 (25945 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 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: 0.574 AC: 87163 AN: 151850 Hom.: 25929 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.574 AC: 87217 AN: 151968 Hom.: 25945 Cov.: 32 AF XY: 0.575 AC XY: 42701 AN XY: 74280

African (AFR) AF: 0.404 AC: 16758 AN: 41442

American (AMR) AF: 0.563 AC: 8606 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2015 AN: 3472

East Asian (EAS) AF: 0.773 AC: 3996 AN: 5168

South Asian (SAS) AF: 0.661 AC: 3182 AN: 4814

European-Finnish (FIN) AF: 0.589 AC: 6210 AN: 10552

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44507 AN: 67930

Other (OTH) AF: 0.591 AC: 1247 AN: 2110

Alfa AF: 0.633 Hom.: 99524

Bravo AF: 0.565

Asia WGS AF: 0.674 AC: 2344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
DANN	Benign	0.62
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1395093; hg19: chr5-10018290;