rs867992

Positions:

• chr10-31100384-A-T

Variant summary

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

The ENST00000658872.1(ENSG00000287564):​n.323-5555A>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 0.401 in 152,124 control chromosomes in the GnomAD database, including 14,228 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 0.40 (14228 hom., cov: 33)
• Consequence: ENST00000658872.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.16

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376481	XR_001747410.3	n.2795-5555A>T		intron_variant, non_coding_transcript_variant
LOC105376481	XR_001747409.3	n.2795-5555A>T		intron_variant, non_coding_transcript_variant
LOC105376481	XR_930796.3	n.904-5555A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000658872.1	n.323-5555A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61046 AN: 152006 Hom.: 14228 Cov.: 33

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.401 AC: 61052 AN: 152124 Hom.: 14228 Cov.: 33 AF XY: 0.406 AC XY: 30231 AN XY: 74376

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.369

Alfa AF: 0.462 Hom.: 2196

Bravo AF: 0.378

Asia WGS AF: 0.360 AC: 1253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs867992; hg19: chr10-31389313;