chr6-151628671-A-C

Variant names:

• chr6-151628671-A-C
• rs6913578
• XR_007059816.1:n.2097A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 22 publications found

Genes affected

LOC124901435 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.480 AC: 19892 AN: 41450

American (AMR) AF: 0.268 AC: 4096 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1124 AN: 3464

East Asian (EAS) AF: 0.326 AC: 1689 AN: 5174

South Asian (SAS) AF: 0.347 AC: 1673 AN: 4820

European-Finnish (FIN) AF: 0.175 AC: 1849 AN: 10584

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21190 AN: 67986

Other (OTH) AF: 0.367 AC: 775 AN: 2114

Alfa AF: 0.328 Hom.: 22733

Bravo AF: 0.358

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.61
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs6913578; hg19: chr6-151949806;