rs10916248

Variant names:

• chr1-224068646-A-T
• rs10916248
• XR_001737824.1:n.242+992A>T

Variant summary

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

The XR_001737824.1(LOC105373061):​n.242+992A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,230 control chromosomes in the GnomAD database, including 2,691 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 0.18 (2691 hom., cov: 33)
• Consequence: LOC105373061 XR_001737824.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160
• Publications: 10 publications found

Genes affected

LOC105373061 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 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: 0.179 AC: 27189 AN: 152112 Hom.: 2691 Cov.: 33

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.179 AC: 27207 AN: 152230 Hom.: 2691 Cov.: 33 AF XY: 0.178 AC XY: 13242 AN XY: 74416

African (AFR) AF: 0.116 AC: 4820 AN: 41542

American (AMR) AF: 0.214 AC: 3271 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 449 AN: 3468

East Asian (EAS) AF: 0.381 AC: 1972 AN: 5174

South Asian (SAS) AF: 0.178 AC: 860 AN: 4830

European-Finnish (FIN) AF: 0.159 AC: 1686 AN: 10600

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13528 AN: 68014

Other (OTH) AF: 0.198 AC: 416 AN: 2106

Alfa AF: 0.184 Hom.: 349

Bravo AF: 0.185

Asia WGS AF: 0.230 AC: 799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.9
DANN	Benign	0.76
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs10916248; hg19: chr1-224256348; COSMIC: COSV50456476;