rs9442384

Variant names:

• chr1-1161907-T-C
• rs9442384
• XR_007065350.1:n.2415T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-1161907-T-C
• chr1-1161907-T-G

Variant summary

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

The XR_007065350.1(LOC124903820):​n.2415T>C 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 0.88 in 152,214 control chromosomes in the GnomAD database, including 59,412 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 0.88 (59412 hom., cov: 34)
• Consequence: LOC124903820 XR_007065350.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 2 publications found

Genes affected

LOC124903820 (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 (NFE) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903820	XR_007065350.1	n.2415T>C		non_coding_transcript_exon_variant	Exon 2 of 2
LOC124903820	XR_007065351.1	n.1697T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133823 AN: 152096 Hom.: 59369 Cov.: 34

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.880 AC: 133924 AN: 152214 Hom.: 59412 Cov.: 34 AF XY: 0.878 AC XY: 65366 AN XY: 74432

African (AFR) AF: 0.818 AC: 33968 AN: 41510

American (AMR) AF: 0.897 AC: 13734 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3150 AN: 3470

East Asian (EAS) AF: 0.597 AC: 3082 AN: 5166

South Asian (SAS) AF: 0.880 AC: 4249 AN: 4828

European-Finnish (FIN) AF: 0.900 AC: 9543 AN: 10606

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.929 AC: 63176 AN: 68010

Other (OTH) AF: 0.873 AC: 1848 AN: 2116

Alfa AF: 0.893 Hom.: 3383

Bravo AF: 0.874

Asia WGS AF: 0.751 AC: 2611 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.29
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9442384; hg19: chr1-1097287;