rs1012123

Positions:

• chr7-10646304-G-A
• chr7-10646304-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_147499.1(MGC4859):​n.64-84727C>T variant causes a intron, non coding transcript 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 NR_147499.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.496

Genes affected

MGC4859 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
MGC4859	NR_147499.1	n.64-84727C>T		intron_variant, non_coding_transcript_variant
LOC107986766	XR_001745090.2	n.277+439G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGC4859	ENST00000634803.1	n.64-84727C>T		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.538

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.510

Alfa AF: 0.442 Hom.: 2520

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1012123; hg19: chr7-10685931;