XR_001738266.2:n.9126A>G

Variant names:

• chr1-160656271-A-G
• rs10218843
• XR_001738266.2:n.9126A>G

Variant summary

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

The XR_001738266.2(LOC107985220):​n.9126A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 152,080 control chromosomes in the GnomAD database, including 10,043 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 (10043 hom., cov: 32)
• Consequence: LOC107985220 XR_001738266.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427
• Publications: 4 publications found

Genes affected

LOC107985220 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985220	XR_001738266.2	n.9126A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228863	ENST00000840727.1	n.50+8936A>G		intron_variant	Intron 1 of 1
ENSG00000309419	ENST00000840926.1	n.58-3402A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54529 AN: 151962 Hom.: 10028 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.359 AC: 54594 AN: 152080 Hom.: 10043 Cov.: 32 AF XY: 0.358 AC XY: 26600 AN XY: 74336

African (AFR) AF: 0.415 AC: 17214 AN: 41442

American (AMR) AF: 0.391 AC: 5979 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 664 AN: 3472

East Asian (EAS) AF: 0.421 AC: 2182 AN: 5186

South Asian (SAS) AF: 0.228 AC: 1099 AN: 4824

European-Finnish (FIN) AF: 0.329 AC: 3481 AN: 10580

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22924 AN: 67974

Other (OTH) AF: 0.335 AC: 707 AN: 2108

Alfa AF: 0.353 Hom.: 5807

Bravo AF: 0.368

Asia WGS AF: 0.323 AC: 1121 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.39
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs10218843; hg19: chr1-160626061;