rs4244437

Positions:

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

Variant summary

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

The NR_037889.1(LOC285626):​n.746-1407G>A 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 0.774 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: LOC285626 NR_037889.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22

Genes affected

LOC285626 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC285626	NR_037889.1	n.746-1407G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000635333.1	n.10G>A		non_coding_transcript_exon_variant	1/8	5
	ENST00000515337.1	n.746-1407G>A		intron_variant, non_coding_transcript_variant		2
	ENST00000641150.1	n.325-1407G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 EAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.750

Gnomad4 OTH exome AF: 0.500

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

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.798

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.759

Alfa AF: 0.744 Hom.: 11495

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4244437; hg19: chr5-158773117;