rs7109645

Positions:

• chr11-77475278-A-C

Variant summary

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

The ENST00000598970.2(ENSG00000268635):​n.1908A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,032 control chromosomes in the GnomAD database, including 6,770 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 0.29 (6769 hom., cov: 32)
  • Exomes 𝑓: 0.32 (1 hom.)
• Consequence: ENST00000598970.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PAK1	XM_024448560.2	c.-301-609T>G		intron_variant			XP_024304328.1
PAK1	XM_047427049.1	c.-301-609T>G		intron_variant			XP_047283005.1
PAK1	XM_047427054.1	c.-301-609T>G		intron_variant			XP_047283010.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000598970.2	n.1908A>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44170 AN: 151880 Hom.: 6765 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.299

GnomAD4 exome AF: 0.324 AC: 11 AN: 34 Hom.: 1 Cov.: 0 AF XY: 0.222 AC XY: 4 AN XY: 18

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.308

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.291 AC: 44197 AN: 151998 Hom.: 6769 Cov.: 32 AF XY: 0.289 AC XY: 21481 AN XY: 74314

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.299

Alfa AF: 0.313 Hom.: 2088

Bravo AF: 0.280

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7109645; hg19: chr11-77186323;