rs3095008

Variant names:

• chr7-20216082-G-A
• rs3095008
• NM_182762.4:c.-218+1217C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-20216082-G-A
• chr7-20216082-G-C
• chr7-20216082-G-T

Variant summary

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

The NM_182762.4(MACC1):​c.-218+1217C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,874 control chromosomes in the GnomAD database, including 18,313 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 0.48 (18313 hom., cov: 31)
• Consequence: MACC1 NM_182762.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 6 publications found

Genes affected

MACC1 (HGNC:30215): (MET transcriptional regulator MACC1) MACC1 is a key regulator of the hepatocyte growth factor (HGF; MIM 142409)-HGF receptor (HGFR, or MET; MIM 164860) pathway, which is involved in cellular growth, epithelial-mesenchymal transition, angiogenesis, cell motility, invasiveness, and metastasis. Expression of MACC1 in colon cancer (MIM 114500) specimens is an independent prognostic indicator for metastasis formation and metastasis-free survival (Stein et al., 2009 [PubMed 19098908]).[supplied by OMIM, Mar 2009]

GIRGL (HGNC:55702): (glutamine insufficiency regulator of glutaminase lncRNA)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MACC1	NM_182762.4	c.-218+1217C>T		intron_variant	Intron 1 of 6	ENST00000400331.10	NP_877439.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MACC1	ENST00000400331.10	c.-218+1217C>T		intron_variant	Intron 1 of 6	2	NM_182762.4	ENSP00000383185.3

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72820 AN: 151756 Hom.: 18292 Cov.: 31

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.480 AC: 72889 AN: 151874 Hom.: 18313 Cov.: 31 AF XY: 0.482 AC XY: 35803 AN XY: 74208

African (AFR) AF: 0.492 AC: 20385 AN: 41452

American (AMR) AF: 0.584 AC: 8907 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1847 AN: 3466

East Asian (EAS) AF: 0.905 AC: 4686 AN: 5180

South Asian (SAS) AF: 0.558 AC: 2682 AN: 4810

European-Finnish (FIN) AF: 0.372 AC: 3919 AN: 10530

Middle Eastern (MID) AF: 0.414 AC: 120 AN: 290

European-Non Finnish (NFE) AF: 0.426 AC: 28905 AN: 67878

Other (OTH) AF: 0.493 AC: 1040 AN: 2110

Alfa AF: 0.452 Hom.: 16110

Bravo AF: 0.498

Asia WGS AF: 0.701 AC: 2427 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.1
DANN	Benign	0.74
PhyloP100		0.014
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3095008; hg19: chr7-20255705;