chr7-10646304-G-A

Variant names:

• chr7-10646304-G-A
• rs1012123
• ENST00000634803.1:n.64-84727C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000634803.1(MGC4859):​n.64-84727C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,872 control chromosomes in the GnomAD database, including 20,656 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 0.52 (20656 hom., cov: 32)
• Consequence: MGC4859 ENST00000634803.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.496
• Publications: 2 publications found

Genes affected

MGC4859 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGC4859	NR_147499.1	n.64-84727C>T		intron_variant	Intron 1 of 2
LOC107986766	XR_001745090.2	n.277+439G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGC4859	ENST00000634803.1	n.64-84727C>T		intron_variant	Intron 1 of 2	1
MGC4859	ENST00000804837.1	n.318+2044C>T		intron_variant	Intron 3 of 3
MGC4859	ENST00000804838.1	n.187-3653C>T		intron_variant	Intron 2 of 2
MGC4859	ENST00000804840.1	n.197+2044C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78403 AN: 151754 Hom.: 20632 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.517 AC: 78480 AN: 151872 Hom.: 20656 Cov.: 32 AF XY: 0.522 AC XY: 38770 AN XY: 74228

African (AFR) AF: 0.538 AC: 22272 AN: 41432

American (AMR) AF: 0.439 AC: 6706 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1423 AN: 3468

East Asian (EAS) AF: 0.713 AC: 3668 AN: 5144

South Asian (SAS) AF: 0.597 AC: 2872 AN: 4808

European-Finnish (FIN) AF: 0.548 AC: 5778 AN: 10552

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.501 AC: 34028 AN: 67888

Other (OTH) AF: 0.510 AC: 1076 AN: 2110

Alfa AF: 0.480 Hom.: 7322

Bravo AF: 0.509

Asia WGS AF: 0.639 AC: 2225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	13
DANN	Benign	0.83
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs1012123; hg19: chr7-10685931;