9-41441099-C-T

Position:

• chr9-41441099-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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

Genes affected

LOC124900272 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=3.984).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900272	XR_007061513.1	n.36461C>T		non_coding_transcript_exon_variant	2/2
LOC107984035	NR_148348.1	n.292-33779C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000692789.2	n.293-61395C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.482

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs711858; hg19: -;