rs10486371

Variant names:

• chr7-19808314-T-C
• rs10486371
• XR_001745112.2:n.1126-2931T>C

Variant summary

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

The XR_001745112.2(LOC107986774):​n.1126-2931T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0527 in 152,142 control chromosomes in the GnomAD database, including 582 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 0.053 (582 hom., cov: 32)
• Consequence: LOC107986774 XR_001745112.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225
• Publications: 0 publications found

Genes affected

LOC107986774 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.214 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: 0.0525 AC: 7983 AN: 152024 Hom.: 574 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0223

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.0275

Gnomad FIN AF: 0.0000943

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00460

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0527 AC: 8013 AN: 152142 Hom.: 582 Cov.: 32 AF XY: 0.0527 AC XY: 3919 AN XY: 74390

African (AFR) AF: 0.143 AC: 5916 AN: 41500

American (AMR) AF: 0.0222 AC: 339 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0159 AC: 55 AN: 3462

East Asian (EAS) AF: 0.225 AC: 1162 AN: 5170

South Asian (SAS) AF: 0.0271 AC: 131 AN: 4832

European-Finnish (FIN) AF: 0.0000943 AC: 1 AN: 10600

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00459 AC: 312 AN: 68008

Other (OTH) AF: 0.0426 AC: 90 AN: 2112

Alfa AF: 0.0206 Hom.: 650

Bravo AF: 0.0587

Asia WGS AF: 0.108 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.41
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs10486371; hg19: chr7-19847937;