2-71731350-C-T

Position:

• chr2-71731350-C-T

Variant summary

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

The XR_007086966.1(LOC124907827):​n.838-11354C>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 0.285 in 152,108 control chromosomes in the GnomAD database, including 6,652 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 0.28 (6652 hom., cov: 32)
• Consequence: LOC124907827 XR_007086966.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

Genes affected

LOC124907827 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124907827	XR_007086966.1	n.838-11354C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43320 AN: 151990 Hom.: 6654 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.285 AC: 43341 AN: 152108 Hom.: 6652 Cov.: 32 AF XY: 0.284 AC XY: 21129 AN XY: 74330

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.256

Alfa AF: 0.306 Hom.: 8571

Bravo AF: 0.270

Asia WGS AF: 0.218 AC: 758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	20
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2900976; hg19: chr2-71958480;