rs7827228

chr8-2732462-A-Cchr8-2732462-A-T

Variant summary

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

The NR_168443.1(LOC105377785):n.538+4969A>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 0.364 in 151,850 control chromosomes in the GnomAD database, including 11,144 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 0.36 (11144 hom., cov: 32)
• Consequence: LOC105377785 NR_168443.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377785	NR_168443.1	n.538+4969A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654515.1	n.531+4969A>C		intron_variant, non_coding_transcript_variant
	ENST00000520024.1	n.176+4969A>C		intron_variant, non_coding_transcript_variant		3
	ENST00000670600.1	n.538+4969A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55205 AN: 151728 Hom.: 11116 Cov.: 32

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.364 AC: 55273 AN: 151850 Hom.: 11144 Cov.: 32 AF XY: 0.360 AC XY: 26686 AN XY: 74194

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.359

Alfa AF: 0.302 Hom.: 5400

Bravo AF: 0.368

Asia WGS AF: 0.401 AC: 1395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.17
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7827228; hg19: chr8-2589993;