rs6005907

Variant names:

• chr22-28831983-G-A
• rs6005907
• ENST00000418292.1:n.35-6877G>A

Variant summary

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

The ENST00000418292.1(ENSG00000226471):​n.35-6877G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,074 control chromosomes in the GnomAD database, including 1,513 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 0.12 (1513 hom., cov: 31)
• Consequence: ENSG00000226471 ENST00000418292.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172

Genes affected

ENSG00000226471 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226471	ENST00000418292.1	n.35-6877G>A		intron_variant	Intron 1 of 1	3
ENSG00000226471	ENST00000458080.1	n.263+9804G>A		intron_variant	Intron 2 of 3	3
ENSG00000226471	ENST00000687270.1	n.258+9804G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17471 AN: 151956 Hom.: 1508 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0704

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.0647

Gnomad FIN AF: 0.0633

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0528

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.115 AC: 17518 AN: 152074 Hom.: 1513 Cov.: 31 AF XY: 0.114 AC XY: 8507 AN XY: 74338

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0704

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.0650

Gnomad4 FIN AF: 0.0633

Gnomad4 NFE AF: 0.0528

Gnomad4 OTH AF: 0.0999

Alfa AF: 0.0661 Hom.: 988

Bravo AF: 0.125

Asia WGS AF: 0.186 AC: 647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6005907; hg19: chr22-29227971;