rs736556

Variant names:

• chr7-31017453-T-C
• rs736556
• XR_001745155.2:n.717-8565T>C

Variant summary

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

The XR_001745155.2(LOC105375222):​n.717-8565T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,210 control chromosomes in the GnomAD database, including 16,101 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 0.36 (16101 hom., cov: 33)
• Consequence: LOC105375222 XR_001745155.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225
• Publications: 4 publications found

Genes affected

LOC105375222 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 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: 0.363 AC: 55278 AN: 152092 Hom.: 16057 Cov.: 33

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.364 AC: 55362 AN: 152210 Hom.: 16101 Cov.: 33 AF XY: 0.356 AC XY: 26513 AN XY: 74432

African (AFR) AF: 0.808 AC: 33540 AN: 41522

American (AMR) AF: 0.230 AC: 3512 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1036 AN: 3470

East Asian (EAS) AF: 0.113 AC: 583 AN: 5174

South Asian (SAS) AF: 0.343 AC: 1655 AN: 4826

European-Finnish (FIN) AF: 0.105 AC: 1113 AN: 10598

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12783 AN: 68002

Other (OTH) AF: 0.351 AC: 742 AN: 2114

Alfa AF: 0.282 Hom.: 1310

Bravo AF: 0.390

Asia WGS AF: 0.288 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.6
DANN	Benign	0.80
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs736556; hg19: chr7-31057068;