rs7969759

chr12-67435923-G-A

Variant summary

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

The XR_001749186.2(LOC105369812):n.1912+9880G>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 0.0706 in 152,200 control chromosomes in the GnomAD database, including 879 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 0.071 (879 hom., cov: 32)
• Consequence: LOC105369812 XR_001749186.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

Genes affected

LOC105369812 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369812	XR_001749186.2	n.1912+9880G>A		intron_variant, non_coding_transcript_variant
LOC105369812	XR_945043.3	n.1912+9880G>A		intron_variant, non_coding_transcript_variant
LOC124903072	XR_007063567.1			upstream_gene_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0705 AC: 10722 AN: 152082 Hom.: 875 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.0358

Gnomad FIN AF: 0.00867

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00204

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0706 AC: 10744 AN: 152200 Hom.: 879 Cov.: 32 AF XY: 0.0728 AC XY: 5414 AN XY: 74410

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.00548

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.0361

Gnomad4 FIN AF: 0.00867

Gnomad4 NFE AF: 0.00203

Gnomad4 OTH AF: 0.0705

Alfa AF: 0.0284 Hom.: 345

Bravo AF: 0.0873

Asia WGS AF: 0.114 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.3
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7969759; hg19: chr12-67829703;