22-40678403-G-C

Position:

• chr22-40678403-G-C

Variant summary

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

The ENST00000688408.2(ENSG00000289292):​n.367+2205C>G 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 0.641 in 149,318 control chromosomes in the GnomAD database, including 31,519 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 0.64 (31519 hom., cov: 26)
• Consequence: ENST00000688408.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.75

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124905123	XR_007068110.1	n.358+2205C>G		intron_variant, non_coding_transcript_variant
LOC124905123	XR_007068109.1	n.4323+2205C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000688408.2	n.367+2205C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.641 AC: 95698 AN: 149204 Hom.: 31482 Cov.: 26

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.641 AC: 95781 AN: 149318 Hom.: 31519 Cov.: 26 AF XY: 0.639 AC XY: 46391 AN XY: 72574

Gnomad4 AFR AF: 0.712

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.976

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.637

Alfa AF: 0.529 Hom.: 1645

Bravo AF: 0.636

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs133068; hg19: chr22-41074407;