rs6901498

Variant names:

• chr6-71735860-G-C
• rs6901498
• ENST00000784456.1:n.131-7871G>C

Variant summary

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

The ENST00000784456.1(ENSG00000302111):​n.131-7871G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,854 control chromosomes in the GnomAD database, including 9,497 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 (9497 hom., cov: 32)
• Consequence: ENSG00000302111 ENST00000784456.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 3 publications found

Genes affected

ENSG00000302111 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000784456.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302111	ENST00000784456.1		n.131-7871G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53041 AN: 151736 Hom.: 9498 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.349 AC: 53053 AN: 151854 Hom.: 9497 Cov.: 32 AF XY: 0.350 AC XY: 25991 AN XY: 74196

African (AFR) AF: 0.277 AC: 11478 AN: 41416

American (AMR) AF: 0.316 AC: 4813 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1431 AN: 3466

East Asian (EAS) AF: 0.337 AC: 1743 AN: 5168

South Asian (SAS) AF: 0.324 AC: 1559 AN: 4814

European-Finnish (FIN) AF: 0.455 AC: 4796 AN: 10530

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26077 AN: 67908

Other (OTH) AF: 0.346 AC: 727 AN: 2102

Alfa AF: 0.379 Hom.: 1358

Bravo AF: 0.333

Asia WGS AF: 0.272 AC: 946 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.57
PhyloP100		-1.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6901498;

hg19: chr6-72445563;