rs3735222

Positions:

• chr7-12570053-G-A

Variant summary

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

The XR_007060635.1(LOC107986768):​n.2175C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,990 control chromosomes in the GnomAD database, including 14,389 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 0.43 (14388 hom., cov: 33)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: LOC107986768 XR_007060635.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330

Genes affected

LOC107986768 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986768	XR_007060635.1	n.2175C>T		non_coding_transcript_exon_variant	3/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65432 AN: 151866 Hom.: 14370 Cov.: 33

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.425

GnomAD4 exome AF: 0.500 AC: 3 AN: 6 Hom.: 1 AF XY: 0.500 AC XY: 3 AN XY: 6

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.431 AC: 65482 AN: 151984 Hom.: 14388 Cov.: 33 AF XY: 0.425 AC XY: 31566 AN XY: 74258

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.421

Alfa AF: 0.425 Hom.: 28616

Bravo AF: 0.434

Asia WGS AF: 0.298 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.3
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3735222; hg19: chr7-12609679;