rs11971770

Variant names:

• chr7-150562663-A-G
• rs11971770
• XM_017012936.2:c.571+550T>C

Variant summary

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

The XM_017012936.2(LOC107986860):​c.571+550T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,050 control chromosomes in the GnomAD database, including 10,836 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 (10836 hom., cov: 32)
• Consequence: LOC107986860 XM_017012936.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.852
• Publications: 2 publications found

Genes affected

LOC107986860 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.589 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: 0.340 AC: 51658 AN: 151932 Hom.: 10802 Cov.: 32

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.340 AC: 51747 AN: 152050 Hom.: 10836 Cov.: 32 AF XY: 0.343 AC XY: 25471 AN XY: 74342

African (AFR) AF: 0.596 AC: 24690 AN: 41452

American (AMR) AF: 0.264 AC: 4026 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 831 AN: 3470

East Asian (EAS) AF: 0.365 AC: 1884 AN: 5168

South Asian (SAS) AF: 0.386 AC: 1861 AN: 4826

European-Finnish (FIN) AF: 0.239 AC: 2527 AN: 10584

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15011 AN: 67954

Other (OTH) AF: 0.302 AC: 638 AN: 2114

Alfa AF: 0.297 Hom.: 1365

Bravo AF: 0.350

Asia WGS AF: 0.380 AC: 1318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.23
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs11971770; hg19: chr7-150259751;