rs7337318

Variant names:

• chr13-20323772-G-C
• rs7337318
• XR_941720.2:n.201-1593G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_941720.2(LOC105370102):​n.201-1593G>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 0 publications found

Genes affected

LOC105370102 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105370102	XR_941720.2	n.201-1593G>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.551 AC: 22802 AN: 41352

American (AMR) AF: 0.540 AC: 8245 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1829 AN: 3470

East Asian (EAS) AF: 0.248 AC: 1279 AN: 5152

South Asian (SAS) AF: 0.540 AC: 2600 AN: 4818

European-Finnish (FIN) AF: 0.513 AC: 5411 AN: 10552

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 40076 AN: 67926

Other (OTH) AF: 0.562 AC: 1184 AN: 2108

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
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs7337318; hg19: chr13-20897911;