rs6456728

Positions:

• chr6-26477551-G-A
• chr6-26477551-G-C

Variant summary

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

The NR_038992.1(LOC285819):​n.1325-70C>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 0.304 in 149,426 control chromosomes in the GnomAD database, including 9,466 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 0.30 (9466 hom., cov: 31)
• Consequence: LOC285819 NR_038992.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC285819	NR_038992.1	n.1325-70C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000707189.1	n.1000-75636G>A		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1001-55154G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45304 AN: 149326 Hom.: 9438 Cov.: 31

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.304 AC: 45375 AN: 149426 Hom.: 9466 Cov.: 31 AF XY: 0.296 AC XY: 21596 AN XY: 72840

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.280

Alfa AF: 0.193 Hom.: 3148

Bravo AF: 0.321

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6456728; hg19: chr6-26477779;