rs10922438

chr1-198500032-G-A

Variant summary

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

The ENST00000660823.1(ENSG00000287989):n.327+19519C>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 0.0873 in 152,070 control chromosomes in the GnomAD database, including 743 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 0.087 (743 hom., cov: 32)
• Consequence: ENST00000660823.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980

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 (SAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371677	XR_922398.3	n.260+19519C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000660823.1	n.327+19519C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0871 AC: 13228 AN: 151952 Hom.: 733 Cov.: 32

Gnomad AFR AF: 0.0989

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0931

Gnomad EAS AF: 0.0971

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0610

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0873 AC: 13273 AN: 152070 Hom.: 743 Cov.: 32 AF XY: 0.0900 AC XY: 6692 AN XY: 74344

Gnomad4 AFR AF: 0.0989

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.0931

Gnomad4 EAS AF: 0.0973

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.0440

Gnomad4 NFE AF: 0.0610

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0751 Hom.: 665

Bravo AF: 0.0935

Asia WGS AF: 0.186 AC: 647 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	0.17
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10922438; hg19: chr1-198469162;