chr7-136841516-G-A

Position:

• chr7-136841516-G-A

Variant summary

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

The ENST00000439694.5(ENSG00000234352):​n.344-55625C>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 0.33 in 152,004 control chromosomes in the GnomAD database, including 8,861 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 0.33 (8861 hom., cov: 33)
• Consequence: ENST00000439694.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.908

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 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
	ENST00000586239.5	n.274-55625C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50066 AN: 151886 Hom.: 8843 Cov.: 33

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.0193

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.330 AC: 50121 AN: 152004 Hom.: 8861 Cov.: 33 AF XY: 0.318 AC XY: 23649 AN XY: 74296

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.0191

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.325

Alfa AF: 0.349 Hom.: 11489

Bravo AF: 0.333

Asia WGS AF: 0.125 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.55
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7811987; hg19: chr7-136526263;