rs7307780

chr12-75826838-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000552856.1(ENSG00000258077):n.296-49308G>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 0.182 in 152,054 control chromosomes in the GnomAD database, including 2,658 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 0.18 (2658 hom., cov: 32)
• Consequence: ENST00000552856.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369844	XR_007063375.1	n.236+7695G>A		intron_variant, non_coding_transcript_variant
LOC105369844	XR_007063374.1	n.236+7695G>A		intron_variant, non_coding_transcript_variant
LOC105369844	XR_007063376.1	n.236+7695G>A		intron_variant, non_coding_transcript_variant
LOC105369844	XR_007063377.1	n.236+7695G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000552856.1	n.296-49308G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27658 AN: 151936 Hom.: 2654 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.182 AC: 27689 AN: 152054 Hom.: 2658 Cov.: 32 AF XY: 0.179 AC XY: 13299 AN XY: 74334

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.177

Alfa AF: 0.178 Hom.: 4424

Bravo AF: 0.185

Asia WGS AF: 0.198 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
Cadd	Benign	8.5
Dann	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7307780; hg19: chr12-76220618;