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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373061	XR_001737824.1	n.242+992A>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;