rs2347699

Positions:

• chr7-134706212-T-A

Variant summary

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

The XR_007060537.1(LOC124901750):​n.29222-86264A>T 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 0.291 in 152,052 control chromosomes in the GnomAD database, including 6,554 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 0.29 (6554 hom., cov: 32)
• Consequence: LOC124901750 XR_007060537.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269

Genes affected

LOC124901750 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901750	XR_007060537.1	n.29222-86264A>T		intron_variant, non_coding_transcript_variant
LOC124901750	XR_007060535.1	n.29222-39122A>T		intron_variant, non_coding_transcript_variant
LOC124901750	XR_007060536.1	n.29222-39122A>T		intron_variant, non_coding_transcript_variant
LOC124901750	XR_007060538.1	n.29222-47502A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44174 AN: 151934 Hom.: 6538 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.291 AC: 44226 AN: 152052 Hom.: 6554 Cov.: 32 AF XY: 0.288 AC XY: 21378 AN XY: 74336

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.281

Alfa AF: 0.288 Hom.: 810

Bravo AF: 0.303

Asia WGS AF: 0.227 AC: 791 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	7.4
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2347699; hg19: chr7-134390964;