rs4244437

Variant names:

• chr5-159346109-G-A
• rs4244437
• ENST00000635333.1:n.10G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-159346109-G-A
• chr5-159346109-G-C
• chr5-159346109-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000765010.1(ENSG00000249738):​n.416G>A 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 0.774 in 152,174 control chromosomes in the GnomAD database, including 46,209 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 0.77 (46205 hom., cov: 32)
  • Exomes 𝑓: 0.75 (4 hom.)
• Consequence: ENSG00000249738 ENST00000765010.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22

Genes affected

ENSG00000249738 (HGNC:58156):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL12B-AS1	NR_037889.1	n.746-1407G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249738	ENST00000635333.1	n.10G>A		non_coding_transcript_exon_variant	Exon 1 of 8	5
ENSG00000249738	ENST00000765010.1	n.416G>A		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000249738	ENST00000765011.1	n.10G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117632 AN: 152040 Hom.: 46148 Cov.: 32

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.757

GnomAD4 exome AF: 0.750 AC: 12 AN: 16 Hom.: 4 Cov.: 0 AF XY: 0.786 AC XY: 11 AN XY: 14

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 9 AN: 12

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.774 AC: 117754 AN: 152158 Hom.: 46205 Cov.: 32 AF XY: 0.781 AC XY: 58069 AN XY: 74390

African (AFR) AF: 0.896 AC: 37232 AN: 41536

American (AMR) AF: 0.798 AC: 12203 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2158 AN: 3470

East Asian (EAS) AF: 0.908 AC: 4680 AN: 5154

South Asian (SAS) AF: 0.824 AC: 3975 AN: 4826

European-Finnish (FIN) AF: 0.771 AC: 8174 AN: 10596

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46893 AN: 67968

Other (OTH) AF: 0.759 AC: 1604 AN: 2112

Alfa AF: 0.750 Hom.: 12965

Bravo AF: 0.780

Asia WGS AF: 0.875 AC: 3045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.66
PhyloP100		1.2

Splicing

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

Publications

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Other links and lift over

dbSNP: rs4244437; hg19: chr5-158773117;