chr9-41441099-C-T

Variant names:

• chr9-41441099-C-T
• rs711858
• XR_007061513.1:n.36461C>T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The XR_007061513.1(LOC124900272):​n.36461C>T 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 0.48 in 136,424 control chromosomes in the GnomAD database, including 18,560 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 0.48 (18560 hom., cov: 22)
• Consequence: LOC124900272 XR_007061513.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 1 publications found

Genes affected

LOC124900272 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=3.984).
• BS2: High Homozygotes in GnomAd4 at 18560 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900272	XR_007061513.1	n.36461C>T		non_coding_transcript_exon_variant	Exon 2 of 2
LOC107984035	NR_148348.1	n.292-33779C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288891	ENST00000692789.3	n.316-61395C>T		intron_variant	Intron 1 of 2
ENSG00000288891	ENST00000792533.1	n.293-38846C>T		intron_variant	Intron 1 of 1
ENSG00000288891	ENST00000792534.1	n.293-33779C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.480 AC: 65448 AN: 136304 Hom.: 18518 Cov.: 22

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.480 AC: 65539 AN: 136424 Hom.: 18560 Cov.: 22 AF XY: 0.480 AC XY: 31789 AN XY: 66284

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.727 AC: 25815 AN: 35524

American (AMR) AF: 0.438 AC: 5809 AN: 13258

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1474 AN: 3224

East Asian (EAS) AF: 0.424 AC: 1860 AN: 4386

South Asian (SAS) AF: 0.581 AC: 2403 AN: 4136

European-Finnish (FIN) AF: 0.368 AC: 3633 AN: 9866

Middle Eastern (MID) AF: 0.464 AC: 115 AN: 248

European-Non Finnish (NFE) AF: 0.369 AC: 23291 AN: 63050

Other (OTH) AF: 0.482 AC: 887 AN: 1842

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.494 Hom.: 1736

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	4.0
DANN	Benign	0.19
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs711858; hg19: -;