rs6935207

Positions:

• chr6-160120141-G-A
• chr6-160120141-G-C
• chr6-160120141-G-T

Variant summary

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

The XR_007059842.1(LOC124901452):​n.854+701C>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 0.292 in 152,106 control chromosomes in the GnomAD database, including 7,050 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 (7050 hom., cov: 33)
• Consequence: LOC124901452 XR_007059842.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

Genes affected

LOC124901452 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901452	XR_007059842.1	n.854+701C>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: 44273 AN: 151988 Hom.: 7030 Cov.: 33

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.292 AC: 44347 AN: 152106 Hom.: 7050 Cov.: 33 AF XY: 0.293 AC XY: 21757 AN XY: 74372

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.272

Alfa AF: 0.122 Hom.: 188

Bravo AF: 0.307

Asia WGS AF: 0.406 AC: 1412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.0
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: rs6935207; hg19: chr6-160541173;