rs7443800

Positions:

• chr5-176132836-G-A

Variant summary

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

The XR_001743014.1(LOC107986487):​n.90+696C>T 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 0.324 in 151,332 control chromosomes in the GnomAD database, including 9,276 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 0.32 (9276 hom., cov: 29)
• Consequence: LOC107986487 XR_001743014.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143

Genes affected

LOC107986487 (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 (NFE) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986487	XR_001743014.1	n.90+696C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000697530.1	n.1220-4325G>A		intron_variant, non_coding_transcript_variant
	ENST00000697531.1	n.655-4325G>A		intron_variant, non_coding_transcript_variant
	ENST00000697534.1	n.622-4325G>A		intron_variant, non_coding_transcript_variant
	ENST00000697538.1	n.321-4325G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49035 AN: 151210 Hom.: 9275 Cov.: 29

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.324 AC: 49047 AN: 151332 Hom.: 9276 Cov.: 29 AF XY: 0.324 AC XY: 23936 AN XY: 73946

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.338

Alfa AF: 0.386 Hom.: 8040

Bravo AF: 0.306

Asia WGS AF: 0.307 AC: 1067 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	6.9
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7443800; hg19: chr5-175559839;