rs10211519

Positions:

• chr2-14830918-A-G
• chr2-14830918-A-T

Variant summary

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

The ENST00000654007.1(ENSG00000287291):​n.857-117623T>C 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 0.437 in 151,978 control chromosomes in the GnomAD database, including 15,805 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 0.44 (15805 hom., cov: 32)
• Consequence: ENST00000654007.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NBAS	XR_007076390.1	n.7016-51771T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654007.1	n.857-117623T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66346 AN: 151860 Hom.: 15791 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.437 AC: 66407 AN: 151978 Hom.: 15805 Cov.: 32 AF XY: 0.438 AC XY: 32526 AN XY: 74264

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.407

Alfa AF: 0.346 Hom.: 12571

Bravo AF: 0.441

Asia WGS AF: 0.417 AC: 1455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10211519; hg19: chr2-14971042;