rs7488647

chr12-131246190-T-Cchr12-131246190-T-G

Variant summary

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

The XR_945559.3(LOC105370082):n.729-7288A>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 0.635 in 151,812 control chromosomes in the GnomAD database, including 31,658 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 0.63 (31658 hom., cov: 31)
• Consequence: LOC105370082 XR_945559.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

Genes affected

LOC105370082 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.24).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370082	XR_945559.3	n.729-7288A>G		intron_variant, non_coding_transcript_variant
LOC105370082	XR_945558.3	n.891-7288A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96203 AN: 151694 Hom.: 31596 Cov.: 31

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.635 AC: 96326 AN: 151812 Hom.: 31658 Cov.: 31 AF XY: 0.629 AC XY: 46674 AN XY: 74158

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.631

Alfa AF: 0.593 Hom.: 25374

Bravo AF: 0.655

Asia WGS AF: 0.509 AC: 1773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
Cadd	Benign	1.3
Dann	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7488647; hg19: chr12-131730735;