rs6912853

Positions:

• chr6-26401210-C-T

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.1000-151977C>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 0.149 in 152,140 control chromosomes in the GnomAD database, including 1,738 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 0.15 (1738 hom., cov: 32)
• Consequence: ENST00000707189.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000707189.1	n.1000-151977C>T		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1001-131495C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22734 AN: 152022 Hom.: 1740 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0795

Gnomad SAS AF: 0.0888

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.149 AC: 22734 AN: 152140 Hom.: 1738 Cov.: 32 AF XY: 0.151 AC XY: 11238 AN XY: 74358

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.0791

Gnomad4 SAS AF: 0.0882

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.133

Alfa AF: 0.145 Hom.: 269

Bravo AF: 0.144

Asia WGS AF: 0.0780 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.4
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6912853; hg19: chr6-26401438;