rs847915

chr7-12494964-C-T

Variant summary

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

The XR_001745093.2(LOC105375156):n.277+554G>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 0.636 in 151,992 control chromosomes in the GnomAD database, including 31,196 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 0.64 (31196 hom., cov: 31)
• Consequence: LOC105375156 XR_001745093.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144

Genes affected

LOC105375156 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375156	XR_001745093.2	n.277+554G>A		intron_variant, non_coding_transcript_variant
LOC102725191	NM_001386512.1	c.-154+7893C>T		intron_variant
LOC105375156	XR_927037.3	n.277+554G>A		intron_variant, non_coding_transcript_variant
LOC105375156	XR_927039.3	n.277+554G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000635746.1	c.-154+7893C>T		intron_variant		5		A2
	ENST00000641054.1	n.376+7893C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96651 AN: 151874 Hom.: 31163 Cov.: 31

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.636 AC: 96729 AN: 151992 Hom.: 31196 Cov.: 31 AF XY: 0.632 AC XY: 46975 AN XY: 74274

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.668

Alfa AF: 0.671 Hom.: 25722

Bravo AF: 0.643

Asia WGS AF: 0.626 AC: 2177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.7
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs847915; hg19: chr7-12534590;