chr7-136841516-G-A

Variant names:

• chr7-136841516-G-A
• rs7811987
• ENST00000439694.6:n.656-55625C>T

Variant summary

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

The ENST00000439694.6(ENSG00000234352):​n.656-55625C>T variant causes a intron 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: ENSG00000234352 ENST00000439694.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.908
• Publications: 3 publications found

Genes affected

ENSG00000234352 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439694.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234352	ENST00000439694.6	TSL:1	n.656-55625C>T		intron	N/A
	ENSG00000234352	ENST00000586239.5	TSL:5	n.274-55625C>T		intron	N/A
	ENSG00000234352	ENST00000592183.5	TSL:4	n.475-55625C>T		intron	N/A

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

African (AFR) AF: 0.392 AC: 16268 AN: 41458

American (AMR) AF: 0.257 AC: 3921 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1084 AN: 3468

East Asian (EAS) AF: 0.0191 AC: 99 AN: 5170

South Asian (SAS) AF: 0.226 AC: 1092 AN: 4824

European-Finnish (FIN) AF: 0.245 AC: 2586 AN: 10566

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23875 AN: 67956

Other (OTH) AF: 0.325 AC: 683 AN: 2104

Alfa AF: 0.349 Hom.: 13270

Bravo AF: 0.333

Asia WGS AF: 0.125 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.55
DANN	Benign	0.70
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs7811987; hg19: chr7-136526263;