rs13306702

Positions:

• chr7-95404734-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_007060439.1(LOC107986822):​n.557+7706C>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 0.0247 in 152,764 control chromosomes in the GnomAD database, including 85 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 0.025 (85 hom., cov: 33)
  • Exomes 𝑓: 0.013 (0 hom.)
• Consequence: LOC107986822 XR_007060439.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801

Genes affected

LOC107986822 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0248 (3772/152288) while in subpopulation AFR AF= 0.0496 (2063/41560). AF 95% confidence interval is 0.0479. There are 85 homozygotes in gnomad4. There are 1805 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 85 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986822	XR_007060439.1	n.557+7706C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0247 AC: 3765 AN: 152170 Hom.: 84 Cov.: 33

Gnomad AFR AF: 0.0497

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0331

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.0144

Gnomad SAS AF: 0.0483

Gnomad FIN AF: 0.00641

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0112

Gnomad OTH AF: 0.0182

GnomAD4 exome AF: 0.0126 AC: 6 AN: 476 Hom.: 0 AF XY: 0.00376 AC XY: 1 AN XY: 266

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0556

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0211

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0248 AC: 3772 AN: 152288 Hom.: 85 Cov.: 33 AF XY: 0.0242 AC XY: 1805 AN XY: 74480

Gnomad4 AFR AF: 0.0496

Gnomad4 AMR AF: 0.0335

Gnomad4 ASJ AF: 0.00634

Gnomad4 EAS AF: 0.0147

Gnomad4 SAS AF: 0.0475

Gnomad4 FIN AF: 0.00641

Gnomad4 NFE AF: 0.0112

Gnomad4 OTH AF: 0.0180

Alfa AF: 0.0197 Hom.: 10

Bravo AF: 0.0289

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.41
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13306702; hg19: chr7-95034046;