rs7709212

chr5-159337169-T-C

Variant summary

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

The NR_037889.1(LOC285626):n.745+4166T>C 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 0.342 in 152,000 control chromosomes in the GnomAD database, including 9,190 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 0.34 (9190 hom., cov: 32)
• Consequence: LOC285626 NR_037889.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

Genes affected

LOC285626 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC285626	NR_037889.1	n.745+4166T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000515337.1	n.745+4166T>C		intron_variant, non_coding_transcript_variant		2
	ENST00000641150.1	n.324+4166T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51947 AN: 151882 Hom.: 9174 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.367

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.342 AC: 51988 AN: 152000 Hom.: 9190 Cov.: 32 AF XY: 0.344 AC XY: 25573 AN XY: 74310

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.368

Alfa AF: 0.347 Hom.: 15568

Bravo AF: 0.353

Asia WGS AF: 0.456 AC: 1585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	11
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7709212; hg19: chr5-158764177;