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 ENST00000684966.2(ENSG00000290922):​n.154T>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: ENSG00000290922 ENST00000684966.2 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000684966.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225720	ENST00000560933.5	TSL:6	n.5T>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000290922	ENST00000684966.2		n.154T>C		non_coding_transcript_exon	Exon 2 of 4
	ENSG00000290922	ENST00000791982.1		n.210T>C		non_coding_transcript_exon	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 v4.9

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;