rs6554759

Variant names:

• chr5-1316987-G-A
• rs6554759

Your query was ambiguous. Multiple possible variants found:

• chr5-1316987-G-A
• chr5-1316987-G-C
• chr5-1316987-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 0.853 in 152,324 control chromosomes in the GnomAD database, including 55,527 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 0.85 (55527 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 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: 0.852 AC: 129747 AN: 152206 Hom.: 55472 Cov.: 35

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.853 AC: 129863 AN: 152324 Hom.: 55527 Cov.: 35 AF XY: 0.853 AC XY: 63509 AN XY: 74496

African (AFR) AF: 0.898 AC: 37337 AN: 41572

American (AMR) AF: 0.875 AC: 13385 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2713 AN: 3472

East Asian (EAS) AF: 0.949 AC: 4931 AN: 5194

South Asian (SAS) AF: 0.917 AC: 4431 AN: 4834

European-Finnish (FIN) AF: 0.773 AC: 8205 AN: 10620

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56115 AN: 68016

Other (OTH) AF: 0.846 AC: 1785 AN: 2110

Alfa AF: 0.838 Hom.: 69276

Bravo AF: 0.862

Asia WGS AF: 0.927 AC: 3223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.39
DANN	Benign	0.63
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs6554759; hg19: chr5-1317102;