7-10436413-T-C

Variant names:

• chr7-10436413-T-C
• rs10269232
• ENST00000804835.1:n.97-26348A>G

Variant summary

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

The ENST00000804835.1(MGC4859):​n.97-26348A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,168 control chromosomes in the GnomAD database, including 4,329 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 0.23 (4329 hom., cov: 33)
• Consequence: MGC4859 ENST00000804835.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184
• Publications: 3 publications found

Genes affected

MGC4859 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804835.1. 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
	MGC4859	ENST00000804835.1		n.97-26348A>G		intron	N/A
	MGC4859	ENST00000804836.1		n.172-16034A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35255 AN: 152050 Hom.: 4333 Cov.: 33

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.232 AC: 35258 AN: 152168 Hom.: 4329 Cov.: 33 AF XY: 0.239 AC XY: 17808 AN XY: 74376

African (AFR) AF: 0.158 AC: 6548 AN: 41542

American (AMR) AF: 0.253 AC: 3866 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 474 AN: 3472

East Asian (EAS) AF: 0.357 AC: 1852 AN: 5186

South Asian (SAS) AF: 0.265 AC: 1277 AN: 4822

European-Finnish (FIN) AF: 0.339 AC: 3583 AN: 10560

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16833 AN: 67988

Other (OTH) AF: 0.232 AC: 489 AN: 2112

Alfa AF: 0.240 Hom.: 2282

Bravo AF: 0.224

Asia WGS AF: 0.279 AC: 972 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.1
DANN	Benign	0.70
PhyloP100		0.18

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: rs10269232;

hg19: chr7-10476040;