rs6729545

Variant names:

• chr2-48806403-C-A
• rs6729545
• XR_001739458.1:n.65-1257C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-48806403-C-A
• chr2-48806403-C-G
• chr2-48806403-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001739458.1(LOC105374594):​n.65-1257C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 151,992 control chromosomes in the GnomAD database, including 9,574 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 0.34 (9574 hom., cov: 32)
• Consequence: LOC105374594 XR_001739458.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 0 publications found

Genes affected

LOC105374594 (HGNC:):

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 = 0.709 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52191 AN: 151874 Hom.: 9574 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.344 AC: 52220 AN: 151992 Hom.: 9574 Cov.: 32 AF XY: 0.347 AC XY: 25802 AN XY: 74288

African (AFR) AF: 0.252 AC: 10453 AN: 41452

American (AMR) AF: 0.317 AC: 4846 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1551 AN: 3466

East Asian (EAS) AF: 0.728 AC: 3755 AN: 5158

South Asian (SAS) AF: 0.441 AC: 2123 AN: 4814

European-Finnish (FIN) AF: 0.345 AC: 3653 AN: 10574

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.365 AC: 24837 AN: 67956

Other (OTH) AF: 0.335 AC: 705 AN: 2104

Alfa AF: 0.339 Hom.: 4202

Bravo AF: 0.335

Asia WGS AF: 0.550 AC: 1911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
DANN	Benign	0.79
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6729545; hg19: chr2-49033542;