9-2194227-C-T

Position:

• chr9-2194227-C-T

Variant summary

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

The XR_007061395.1(LOC107987043):​n.302-13205G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 152,118 control chromosomes in the GnomAD database, including 45,613 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 0.77 (45613 hom., cov: 32)
• Consequence: LOC107987043 XR_007061395.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.814

Genes affected

LOC107987043 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987043	XR_007061395.1	n.302-13205G>A		intron_variant, non_coding_transcript_variant
LOC107987043	XR_001746600.2	n.298-13205G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117288 AN: 152000 Hom.: 45558 Cov.: 32

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.772 AC: 117406 AN: 152118 Hom.: 45613 Cov.: 32 AF XY: 0.774 AC XY: 57579 AN XY: 74358

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.828

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.731

Gnomad4 OTH AF: 0.776

Alfa AF: 0.734 Hom.: 51860

Bravo AF: 0.781

Asia WGS AF: 0.741 AC: 2576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.47
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4741652; hg19: chr9-2194227; COSMIC: COSV56648857;