11-72197581-T-A

Position:

• chr11-72197581-T-A

Variant summary

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

The ENST00000378140.3(ENSG00000204971):​n.419+932A>T 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 0.23 in 152,152 control chromosomes in the GnomAD database, including 4,988 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 0.23 (4988 hom., cov: 32)
• Consequence: ENST00000378140.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000378140.3	n.419+932A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34866 AN: 152034 Hom.: 4962 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.230 AC: 34932 AN: 152152 Hom.: 4988 Cov.: 32 AF XY: 0.236 AC XY: 17541 AN XY: 74398

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.198

Alfa AF: 0.0824 Hom.: 123

Bravo AF: 0.231

Asia WGS AF: 0.369 AC: 1283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.62
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11235462; hg19: chr11-71908625;