6-151628671-A-C

Position:

• chr6-151628671-A-C

Variant summary

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

The XR_007059816.1(LOC124901435):​n.2097A>C 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 0.346 in 152,084 control chromosomes in the GnomAD database, including 9,806 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 0.35 (9806 hom., cov: 32)
• Consequence: LOC124901435 XR_007059816.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526

Genes affected

LOC124901435 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901435	XR_007059816.1	n.2097A>C		non_coding_transcript_exon_variant	1/2
		n.151628671A>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52619 AN: 151966 Hom.: 9798 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.346 AC: 52649 AN: 152084 Hom.: 9806 Cov.: 32 AF XY: 0.340 AC XY: 25259 AN XY: 74360

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.367

Alfa AF: 0.318 Hom.: 12287

Bravo AF: 0.358

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6913578; hg19: chr6-151949806;