rs139271

Variant names:

• chr22-39091590-T-C
• rs139271
• ENST00000560933.5:n.5T>C

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000225720 ENST00000560933.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 3 publications found

Genes affected

ENSG00000225720 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC101927202	XR_007068102.1	n.125T>C		non_coding_transcript_exon_variant	Exon 2 of 4
LOC101927202	XR_938259.3	n.529T>C		non_coding_transcript_exon_variant	Exon 1 of 2
LOC101927202	XR_007068103.1	n.60-17T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225720	ENST00000560933.5	n.5T>C		non_coding_transcript_exon_variant	Exon 1 of 2	6
ENSG00000290922	ENST00000684966.2	n.154T>C		non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000290922	ENST00000791982.1	n.210T>C		non_coding_transcript_exon_variant	Exon 1 of 3

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

African (AFR) AF: 0.900 AC: 9 AN: 10

American (AMR) AF: 0.300 AC: 3 AN: 10

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.400 AC: 4 AN: 10

South Asian (SAS) AF: 0.500 AC: 14 AN: 28

European-Finnish (FIN) AF: 0.656 AC: 286 AN: 436

Middle Eastern (MID) AF: 0.625 AC: 5 AN: 8

European-Non Finnish (NFE) AF: 0.583 AC: 155 AN: 266

Other (OTH) AF: 0.554 AC: 31 AN: 56

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

African (AFR) AF: 0.852 AC: 35298 AN: 41430

American (AMR) AF: 0.414 AC: 6322 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1627 AN: 3466

East Asian (EAS) AF: 0.357 AC: 1839 AN: 5156

South Asian (SAS) AF: 0.461 AC: 2220 AN: 4818

European-Finnish (FIN) AF: 0.524 AC: 5523 AN: 10532

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30494 AN: 67946

Other (OTH) AF: 0.501 AC: 1054 AN: 2102

Alfa AF: 0.568 Hom.: 4020

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs139271; hg19: chr22-39487595;