rs139271

chr22-39091590-T-C

Variant summary

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

The ENST00000560933.5(ENSG00000225720):n.5T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 152,736 control chromosomes in the GnomAD database, including 26,538 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 0.56 (26381 hom., cov: 31)
  • Exomes 𝑓: 0.62 (157 hom.)
• Consequence: ENST00000560933.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927202	XR_938259.3	n.529T>C		non_coding_transcript_exon_variant	1/2
LOC101927202	XR_007068102.1	n.125T>C		non_coding_transcript_exon_variant	2/4
LOC101927202	XR_007068103.1	n.60-17T>C		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000560933.5	n.5T>C		non_coding_transcript_exon_variant	1/2
	ENST00000684966.1	n.126T>C		non_coding_transcript_exon_variant	2/4
	ENST00000424436.2	n.60-17T>C		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84828 AN: 151792 Hom.: 26327 Cov.: 31

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.506

GnomAD4 exome AF: 0.615 AC: 508 AN: 826 Hom.: 157 Cov.: 0 AF XY: 0.602 AC XY: 277 AN XY: 460

Gnomad4 AFR exome AF: 0.900

Gnomad4 AMR exome AF: 0.300

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.400

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.656

Gnomad4 NFE exome AF: 0.583

Gnomad4 OTH exome AF: 0.554

GnomAD4 genome AF: 0.559 AC: 84936 AN: 151910 Hom.: 26381 Cov.: 31 AF XY: 0.557 AC XY: 41304 AN XY: 74212

Gnomad4 AFR AF: 0.852

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.501

Alfa AF: 0.557 Hom.: 3725

Bravo AF: 0.561

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.42
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs139271; hg19: chr22-39487595;