rs788748

chr7-45986582-A-Gchr7-45986582-A-T

Variant summary

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

The XR_001745202.2(LOC102723446):n.831-3951A>G 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 0.591 in 152,058 control chromosomes in the GnomAD database, including 27,561 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 0.59 (27561 hom., cov: 32)
• Consequence: LOC102723446 XR_001745202.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179

Genes affected

LOC102723446 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723446	XR_001745202.2	n.831-3951A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89763 AN: 151940 Hom.: 27529 Cov.: 32

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.914

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.591 AC: 89848 AN: 152058 Hom.: 27561 Cov.: 32 AF XY: 0.592 AC XY: 44003 AN XY: 74312

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.913

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.582

Alfa AF: 0.522 Hom.: 28493

Bravo AF: 0.596

Asia WGS AF: 0.734 AC: 2550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.76
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs788748; hg19: chr7-46026181;