rs6005907

Positions:

• chr22-28831983-G-A

Variant summary

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

The ENST00000458080.1(ENSG00000226471):​n.263+9804G>A variant causes a intron, non coding transcript 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: ENST00000458080.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000458080.1	n.263+9804G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000418292.1	n.35-6877G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000687270.1	n.258+9804G>A		intron_variant, non_coding_transcript_variant

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;