chr11-38924616-G-A

Variant names:

• chr11-38924616-G-A
• rs7947387
• ENST00000722718.1:n.439-45256C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000722718.1(ENSG00000285751):​n.439-45256C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.039 in 151,814 control chromosomes in the GnomAD database, including 168 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 0.039 (168 hom., cov: 32)
• Consequence: ENSG00000285751 ENST00000722718.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608
• Publications: 1 publications found

Genes affected

ENSG00000285751 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0582 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722718.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285751	ENST00000722718.1		n.439-45256C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0390 AC: 5921 AN: 151696 Hom.: 169 Cov.: 32

Gnomad AFR AF: 0.0117

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0391

Gnomad ASJ AF: 0.0736

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0144

Gnomad FIN AF: 0.0225

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.0503

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

GnomAD4 genome AF: 0.0390 AC: 5914 AN: 151814 Hom.: 168 Cov.: 32 AF XY: 0.0370 AC XY: 2744 AN XY: 74200

African (AFR) AF: 0.0117 AC: 485 AN: 41412

American (AMR) AF: 0.0391 AC: 596 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0736 AC: 255 AN: 3466

East Asian (EAS) AF: 0.000388 AC: 2 AN: 5156

South Asian (SAS) AF: 0.0140 AC: 67 AN: 4798

European-Finnish (FIN) AF: 0.0225 AC: 236 AN: 10480

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0597 AC: 4055 AN: 67930

Other (OTH) AF: 0.0498 AC: 105 AN: 2108

Alfa AF: 0.0521 Hom.: 262

Bravo AF: 0.0400

Asia WGS AF: 0.00751 AC: 26 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.77
DANN	Benign	0.76
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs7947387; hg19: chr11-38946166;