rs10497464

Positions:

• chr2-177071787-T-C

Variant summary

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

The ENST00000441205.1(ENSG00000236501):​n.370+22788A>G 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 0.0386 in 152,240 control chromosomes in the GnomAD database, including 289 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 0.039 (289 hom., cov: 32)
• Consequence: ENST00000441205.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.883

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373760	XR_001739795.1	n.1482-7013A>G		intron_variant, non_coding_transcript_variant
LOC105373760	XR_001739796.1	n.381-7013A>G		intron_variant, non_coding_transcript_variant
LOC105373760	XR_923622.2	n.358-7013A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000441205.1	n.370+22788A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0386 AC: 5878 AN: 152122 Hom.: 286 Cov.: 32

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.0882

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.0378

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0126

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0386 AC: 5884 AN: 152240 Hom.: 289 Cov.: 32 AF XY: 0.0432 AC XY: 3213 AN XY: 74440

Gnomad4 AFR AF: 0.0302

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.0527

Gnomad4 EAS AF: 0.0876

Gnomad4 SAS AF: 0.0458

Gnomad4 FIN AF: 0.0378

Gnomad4 NFE AF: 0.0126

Gnomad4 OTH AF: 0.0473

Alfa AF: 0.0202 Hom.: 66

Bravo AF: 0.0462

Asia WGS AF: 0.0660 AC: 230 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497464; hg19: chr2-177936515;