7-46001501-A-G

Position:

• chr7-46001501-A-G

Variant summary

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

The XR_001745204.2(LOC105375264):​n.145-5369T>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 0.766 in 152,124 control chromosomes in the GnomAD database, including 45,048 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 0.77 (45048 hom., cov: 33)
• Consequence: LOC105375264 XR_001745204.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

LOC105375264 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375264	XR_001745204.2	n.145-5369T>C		intron_variant, non_coding_transcript_variant
LOC102723446	XR_007060314.1	n.1269+10424A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116514 AN: 152006 Hom.: 45020 Cov.: 33

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.883

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.766 AC: 116598 AN: 152124 Hom.: 45048 Cov.: 33 AF XY: 0.764 AC XY: 56835 AN XY: 74358

Gnomad4 AFR AF: 0.743

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.883

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.886

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.768

Gnomad4 OTH AF: 0.805

Alfa AF: 0.776 Hom.: 44306

Bravo AF: 0.768

Asia WGS AF: 0.924 AC: 3207 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.8
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: rs788740; hg19: chr7-46041100;