rs12699509

Positions:

• chr7-13521970-G-A

Variant summary

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

The ENST00000639998.1(ENSG00000229618):​n.723-114676G>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 0.206 in 151,972 control chromosomes in the GnomAD database, including 3,876 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 0.21 (3876 hom., cov: 32)
• Consequence: ENST00000639998.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.504

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986770	XR_001745097.2	n.148-180346G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000639998.1	n.723-114676G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31279 AN: 151854 Hom.: 3873 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0827

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.206 AC: 31290 AN: 151972 Hom.: 3876 Cov.: 32 AF XY: 0.201 AC XY: 14927 AN XY: 74262

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.00213

Gnomad4 SAS AF: 0.0832

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.223

Alfa AF: 0.233 Hom.: 1206

Bravo AF: 0.198

Asia WGS AF: 0.0500 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.67
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12699509; hg19: chr7-13561595;