1-232948998-T-C

Variant names:

• chr1-232948998-T-C
• rs3820124
• XR_001738525.2:n.2381A>G

Variant summary

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

The XR_001738525.2(LOC107985361):​n.2381A>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 0.243 in 152,126 control chromosomes in the GnomAD database, including 4,589 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 0.24 (4589 hom., cov: 32)
• Consequence: LOC107985361 XR_001738525.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 16 publications found

Genes affected

LOC107985361 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985361	XR_001738525.2	n.2381A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303568	ENST00000795688.1	n.255-649A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36900 AN: 152008 Hom.: 4569 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.243 AC: 36966 AN: 152126 Hom.: 4589 Cov.: 32 AF XY: 0.240 AC XY: 17837 AN XY: 74350

African (AFR) AF: 0.307 AC: 12741 AN: 41462

American (AMR) AF: 0.183 AC: 2794 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 949 AN: 3468

East Asian (EAS) AF: 0.205 AC: 1064 AN: 5184

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

European-Finnish (FIN) AF: 0.186 AC: 1966 AN: 10580

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15573 AN: 68000

Other (OTH) AF: 0.246 AC: 520 AN: 2112

Alfa AF: 0.236 Hom.: 13642

Bravo AF: 0.245

Asia WGS AF: 0.240 AC: 836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.68
DANN	Benign	0.25
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs3820124; hg19: chr1-233084744;