rs10173407

Positions:

• chr2-237959554-C-T

Variant summary

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

The ENST00000686788.1(ENSG00000288857):​n.259+2918G>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 0.35 in 152,126 control chromosomes in the GnomAD database, including 9,410 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 0.35 (9410 hom., cov: 33)
• Consequence: ENST00000686788.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124908001	XR_007088146.1	n.627-2213C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000686788.1	n.259+2918G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53215 AN: 152008 Hom.: 9411 Cov.: 33

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.350 AC: 53217 AN: 152126 Hom.: 9410 Cov.: 33 AF XY: 0.350 AC XY: 26052 AN XY: 74360

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.373

Alfa AF: 0.373 Hom.: 5460

Bravo AF: 0.347

Asia WGS AF: 0.334 AC: 1165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10173407; hg19: chr2-238868196;