2-99306504-C-T

Position:

• chr2-99306504-C-T

Variant summary

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

The XR_007087152.1(LOC107985923):​n.126-14622C>T 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 0.602 in 151,494 control chromosomes in the GnomAD database, including 28,214 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 0.60 (28214 hom., cov: 32)
• Consequence: LOC107985923 XR_007087152.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652

Genes affected

LOC107985923 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985923	XR_007087152.1	n.126-14622C>T		intron_variant, non_coding_transcript_variant
TXNDC9	XM_017003147.3	c.*269G>A		3_prime_UTR_variant	5/5

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.602 AC: 91160 AN: 151374 Hom.: 28206 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.602 AC: 91196 AN: 151494 Hom.: 28214 Cov.: 32 AF XY: 0.601 AC XY: 44480 AN XY: 74000

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.819

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.657

Alfa AF: 0.651 Hom.: 15387

Bravo AF: 0.604

Asia WGS AF: 0.646 AC: 2250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.23

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6722617; hg19: chr2-99922967; COSMIC: COSV68215278;