rs4516942

Variant names:

• chr6-54770619-G-A
• rs4516942
• ENST00000407852.2:n.37G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-54770619-G-A
• chr6-54770619-G-T

Variant summary

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

The ENST00000407852.2(KRASP1):​n.37G>A variant causes a non coding transcript exon change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.629 in 673,486 control chromosomes in the GnomAD database, including 139,109 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 0.69 (37330 hom., cov: 31)
  • Exomes 𝑓: 0.61 (101779 hom.)
• Consequence: KRASP1 ENST00000407852.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.21
• 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=-0.5).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KRASP1		n.54770619G>A		intragenic_variant
LOC107986606	XR_001744176.3	n.95+31118C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KRASP1	ENST00000407852.2	n.37G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000299445	ENST00000763589.1	n.132+31118C>T		intron_variant	Intron 1 of 6
ENSG00000299445	ENST00000763590.1	n.87+31118C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.687 AC: 104405 AN: 151908 Hom.: 37291 Cov.: 31

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.660

GnomAD4 exome AF: 0.612 AC: 319067 AN: 521460 Hom.: 101779 Cov.: 0 AF XY: 0.621 AC XY: 177077 AN XY: 285130

African (AFR) AF: 0.855 AC: 12349 AN: 14442

American (AMR) AF: 0.393 AC: 15345 AN: 39006

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 11760 AN: 17442

East Asian (EAS) AF: 0.296 AC: 9317 AN: 31484

South Asian (SAS) AF: 0.695 AC: 45084 AN: 64906

European-Finnish (FIN) AF: 0.590 AC: 25034 AN: 42422

Middle Eastern (MID) AF: 0.734 AC: 2263 AN: 3084

European-Non Finnish (NFE) AF: 0.642 AC: 180911 AN: 281816

Other (OTH) AF: 0.633 AC: 17004 AN: 26858

GnomAD4 genome AF: 0.687 AC: 104491 AN: 152026 Hom.: 37330 Cov.: 31 AF XY: 0.679 AC XY: 50458 AN XY: 74308

African (AFR) AF: 0.867 AC: 35963 AN: 41488

American (AMR) AF: 0.502 AC: 7665 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2358 AN: 3470

East Asian (EAS) AF: 0.323 AC: 1662 AN: 5142

South Asian (SAS) AF: 0.654 AC: 3154 AN: 4820

European-Finnish (FIN) AF: 0.599 AC: 6322 AN: 10560

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 45020 AN: 67960

Other (OTH) AF: 0.659 AC: 1390 AN: 2110

Alfa AF: 0.674 Hom.: 17823

Bravo AF: 0.683

Asia WGS AF: 0.530 AC: 1845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	3.8
DANN	Benign	0.43
PhyloP100		7.2

Splicing

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

Other links and lift over

dbSNP: rs4516942; hg19: chr6-54635417;