chr7-113687111-G-A

Variant names:

• chr7-113687111-G-A
• rs2396676
• ENST00000810746.1:n.263+35445C>T

Variant summary

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

The ENST00000810746.1(ENSG00000305398):​n.263+35445C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 152,004 control chromosomes in the GnomAD database, including 16,809 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 0.40 (16809 hom., cov: 32)
• Consequence: ENSG00000305398 ENST00000810746.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 7 publications found

Genes affected

ENSG00000305398 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810746.1. 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
	ENSG00000305398	ENST00000810746.1		n.263+35445C>T		intron	N/A
	ENSG00000305398	ENST00000810747.1		n.106+35445C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60476 AN: 151886 Hom.: 16755 Cov.: 32

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.399 AC: 60605 AN: 152004 Hom.: 16809 Cov.: 32 AF XY: 0.396 AC XY: 29438 AN XY: 74308

African (AFR) AF: 0.791 AC: 32825 AN: 41484

American (AMR) AF: 0.349 AC: 5331 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1076 AN: 3464

East Asian (EAS) AF: 0.292 AC: 1510 AN: 5170

South Asian (SAS) AF: 0.312 AC: 1505 AN: 4824

European-Finnish (FIN) AF: 0.248 AC: 2614 AN: 10540

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14699 AN: 67952

Other (OTH) AF: 0.376 AC: 795 AN: 2112

Alfa AF: 0.279 Hom.: 25254

Bravo AF: 0.425

Asia WGS AF: 0.339 AC: 1180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.034
DANN	Benign	0.41
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2396676;

hg19: chr7-113327166;