rs617022

Positions:

• chr12-5194396-A-G

Variant summary

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

The XR_931577.2(LOC105369617):​n.768+22507A>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 0.351 in 152,112 control chromosomes in the GnomAD database, including 9,523 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 0.35 (9523 hom., cov: 33)
• Consequence: LOC105369617 XR_931577.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23

Genes affected

LOC124902864 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902864	XR_007063179.1	n.147+1254T>C		intron_variant, non_coding_transcript_variant
LOC105369617	XR_931577.2	n.768+22507A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53377 AN: 151992 Hom.: 9515 Cov.: 33

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.351 AC: 53402 AN: 152112 Hom.: 9523 Cov.: 33 AF XY: 0.349 AC XY: 25968 AN XY: 74362

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.361

Alfa AF: 0.365 Hom.: 2523

Bravo AF: 0.351

Asia WGS AF: 0.397 AC: 1383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.037
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs617022; hg19: chr12-5303562;