2-156348594-T-A

Position:

• chr2-156348594-T-A

Variant summary

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

The XR_007088691.1(LOC124906082):​n.134+1353T>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 0.139 in 152,232 control chromosomes in the GnomAD database, including 2,396 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 0.14 (2396 hom., cov: 33)
• Consequence: LOC124906082 XR_007088691.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41

Genes affected

LOC124906082 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124906082	XR_007088691.1	n.134+1353T>A		intron_variant, non_coding_transcript_variant
LOC124906082	XR_007088690.1	n.97+1237T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21177 AN: 152112 Hom.: 2392 Cov.: 33

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.0701

Gnomad FIN AF: 0.0626

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0768

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.139 AC: 21213 AN: 152232 Hom.: 2396 Cov.: 33 AF XY: 0.135 AC XY: 10064 AN XY: 74438

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.0958

Gnomad4 ASJ AF: 0.0352

Gnomad4 EAS AF: 0.00327

Gnomad4 SAS AF: 0.0695

Gnomad4 FIN AF: 0.0626

Gnomad4 NFE AF: 0.0768

Gnomad4 OTH AF: 0.109

Alfa AF: 0.117 Hom.: 211

Bravo AF: 0.151

Asia WGS AF: 0.0490 AC: 170 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	13
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1466408; hg19: chr2-157205106;