rs17528240

Variant names:

• chr7-10710287-T-C
• rs17528240
• ENST00000634803.1:n.63+69595A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-10710287-T-C
• chr7-10710287-T-G

Variant summary

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

The ENST00000634803.1(MGC4859):​n.63+69595A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,056 control chromosomes in the GnomAD database, including 3,617 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 0.21 (3617 hom., cov: 32)
• Consequence: MGC4859 ENST00000634803.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGC4859	NR_147499.1	n.63+69595A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGC4859	ENST00000634803.1	n.63+69595A>G		intron_variant	Intron 1 of 2	1
MGC4859	ENST00000804837.1	n.196+23945A>G		intron_variant	Intron 2 of 3
MGC4859	ENST00000804838.1	n.186+23945A>G		intron_variant	Intron 2 of 2
MGC4859	ENST00000804839.1	n.287+23843A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32424 AN: 151938 Hom.: 3616 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.213 AC: 32448 AN: 152056 Hom.: 3617 Cov.: 32 AF XY: 0.212 AC XY: 15730 AN XY: 74296

African (AFR) AF: 0.206 AC: 8553 AN: 41474

American (AMR) AF: 0.152 AC: 2313 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 933 AN: 3472

East Asian (EAS) AF: 0.240 AC: 1241 AN: 5166

South Asian (SAS) AF: 0.182 AC: 877 AN: 4826

European-Finnish (FIN) AF: 0.207 AC: 2184 AN: 10576

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15621 AN: 67956

Other (OTH) AF: 0.210 AC: 443 AN: 2114

Alfa AF: 0.213 Hom.: 4929

Bravo AF: 0.210

Asia WGS AF: 0.214 AC: 744 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.57
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs17528240; hg19: chr7-10749914;