chr7-86172914-A-G

Variant names:

• chr7-86172914-A-G
• rs12704232
• ENST00000757672.1:n.144+11495T>C

Variant summary

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

The ENST00000757672.1(ENSG00000298738):​n.144+11495T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,028 control chromosomes in the GnomAD database, including 1,661 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 0.14 (1661 hom., cov: 32)
• Consequence: ENSG00000298738 ENST00000757672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370
• Publications: 2 publications found

Genes affected

ENSG00000298738 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757672.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298738	ENST00000757672.1		n.144+11495T>C		intron	N/A
	ENSG00000298738	ENST00000757673.1		n.143+11495T>C		intron	N/A
	ENSG00000298738	ENST00000757674.1		n.143+11495T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21746 AN: 151910 Hom.: 1662 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0805

Gnomad EAS AF: 0.0753

Gnomad SAS AF: 0.0536

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.143 AC: 21739 AN: 152028 Hom.: 1661 Cov.: 32 AF XY: 0.144 AC XY: 10694 AN XY: 74304

African (AFR) AF: 0.163 AC: 6776 AN: 41532

American (AMR) AF: 0.144 AC: 2205 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0805 AC: 279 AN: 3466

East Asian (EAS) AF: 0.0760 AC: 394 AN: 5184

South Asian (SAS) AF: 0.0532 AC: 257 AN: 4830

European-Finnish (FIN) AF: 0.225 AC: 2378 AN: 10574

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8951 AN: 67850

Other (OTH) AF: 0.129 AC: 271 AN: 2108

Alfa AF: 0.131 Hom.: 704

Bravo AF: 0.140

Asia WGS AF: 0.0780 AC: 270 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.60
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs12704232; hg19: chr7-85802230;