rs6913881

Variant names:

• chr6-54774193-G-A
• rs6913881

Variant summary

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

The variant allele was found at a frequency of 0.352 in 152,012 control chromosomes in the GnomAD database, including 13,618 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 (13618 hom., cov: 32)
• Consequence: KRASP1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 3 publications found

Genes affected

KRASP1 (HGNC:6406): (KRAS proto-oncogene, GTPase pseudogene 1)

ENSG00000299445 (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 (AFR) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000763589.1. 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
	ENSG00000299445	ENST00000763589.1		n.132+27544C>T		intron	N/A
	ENSG00000299445	ENST00000763590.1		n.87+27544C>T		intron	N/A
	ENSG00000299445	ENST00000763591.1		n.69+27544C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53437 AN: 151894 Hom.: 13579 Cov.: 32

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.352 AC: 53532 AN: 152012 Hom.: 13618 Cov.: 32 AF XY: 0.345 AC XY: 25638 AN XY: 74332

African (AFR) AF: 0.727 AC: 30142 AN: 41458

American (AMR) AF: 0.242 AC: 3687 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 973 AN: 3464

East Asian (EAS) AF: 0.144 AC: 743 AN: 5168

South Asian (SAS) AF: 0.254 AC: 1225 AN: 4814

European-Finnish (FIN) AF: 0.138 AC: 1462 AN: 10562

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14279 AN: 67968

Other (OTH) AF: 0.334 AC: 707 AN: 2114

Alfa AF: 0.284 Hom.: 1248

Bravo AF: 0.374

Asia WGS AF: 0.275 AC: 958 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.96
DANN	Benign	0.32
PhyloP100		-0.027

Splicing

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

Other links and lift over

dbSNP: rs6913881; hg19: chr6-54638991; COSMIC: COSV68338957;