rs7337318

Positions:

• chr13-20323772-G-C

Variant summary

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

The XR_941720.2(LOC105370102):​n.201-1593G>C 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 0.554 in 151,848 control chromosomes in the GnomAD database, including 23,622 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 0.55 (23622 hom., cov: 31)
• Consequence: LOC105370102 XR_941720.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

Genes affected

LOC105370102 (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 (NFE) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370102	XR_941720.2	n.201-1593G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84058 AN: 151730 Hom.: 23594 Cov.: 31

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.554 AC: 84145 AN: 151848 Hom.: 23622 Cov.: 31 AF XY: 0.547 AC XY: 40582 AN XY: 74226

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.562

Alfa AF: 0.568 Hom.: 3048

Bravo AF: 0.553

Asia WGS AF: 0.467 AC: 1627 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	0.032
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7337318; hg19: chr13-20897911;