rs759171

Variant names:

• chr7-55018519-A-C
• rs759171
• XR_007060329.1:n.404T>G

Your query was ambiguous. Multiple possible variants found:

• chr7-55018519-A-C
• chr7-55018519-A-G

Variant summary

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

The XR_007060329.1(LOC105375284):​n.404T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.853 in 152,136 control chromosomes in the GnomAD database, including 55,417 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 (55417 hom., cov: 32)
• Consequence: LOC105375284 XR_007060329.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 10 publications found

Genes affected

LOC105375284 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.853 AC: 129697 AN: 152018 Hom.: 55390 Cov.: 32

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.879

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

GnomAD4 genome AF: 0.853 AC: 129779 AN: 152136 Hom.: 55417 Cov.: 32 AF XY: 0.852 AC XY: 63340 AN XY: 74358

African (AFR) AF: 0.841 AC: 34910 AN: 41530

American (AMR) AF: 0.809 AC: 12366 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.896 AC: 3110 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5119 AN: 5130

South Asian (SAS) AF: 0.951 AC: 4585 AN: 4822

European-Finnish (FIN) AF: 0.825 AC: 8738 AN: 10596

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 57964 AN: 67986

Other (OTH) AF: 0.877 AC: 1851 AN: 2110

Alfa AF: 0.854 Hom.: 8320

Bravo AF: 0.851

Asia WGS AF: 0.949 AC: 3300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.24
PhyloP100		-1.1
PromoterAI		0.0027	Neutral

Splicing

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

Other links and lift over

dbSNP: rs759171; hg19: chr7-55086212; COSMIC: COSV51842751;