22-38897180-A-G

Variant summary

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

The ENST00000656940.1(ENSG00000288106):n.172-3867A>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 0.705 in 152,184 control chromosomes in the GnomAD database, including 39,535 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 0.71 (39535 hom., cov: 33)
• Consequence: ENST00000656940.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

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 (AFR) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373032	XR_938256.2	n.721+10173A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656940.1	n.172-3867A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107209 AN: 152066 Hom.: 39486 Cov.: 33

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.705 AC: 107306 AN: 152184 Hom.: 39535 Cov.: 33 AF XY: 0.702 AC XY: 52205 AN XY: 74396

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.676

Alfa AF: 0.656 Hom.: 3931

Bravo AF: 0.705

Asia WGS AF: 0.745 AC: 2592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	6.4
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs132515; hg19: chr22-39293185;