rs6912853

Variant names:

• chr6-26401210-C-T
• rs6912853
• ENST00000707189.1:n.1000-151977C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000707189.1(ENSG00000291336):​n.1000-151977C>T variant causes a intron 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: ENSG00000291336 ENST00000707189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 11 publications found

Genes affected

ENSG00000291336 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000707189.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291336	ENST00000707189.1		n.1000-151977C>T		intron	N/A
	ENSG00000291338	ENST00000707191.1		n.1001-131495C>T		intron	N/A

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

African (AFR) AF: 0.136 AC: 5659 AN: 41476

American (AMR) AF: 0.135 AC: 2065 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 426 AN: 3472

East Asian (EAS) AF: 0.0791 AC: 410 AN: 5186

South Asian (SAS) AF: 0.0882 AC: 425 AN: 4818

European-Finnish (FIN) AF: 0.232 AC: 2450 AN: 10558

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10841 AN: 68008

Other (OTH) AF: 0.133 AC: 282 AN: 2116

Alfa AF: 0.145 Hom.: 760

Bravo AF: 0.144

Asia WGS AF: 0.0780 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.4
DANN	Benign	0.56
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs6912853; hg19: chr6-26401438;