chr7-20047359-C-G

Variant names:

• chr7-20047359-C-G
• rs6954796
• ENST00000415499.6:n.112-1798G>C

Variant summary

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

The ENST00000435968.5(MACC1-OT1):​n.59-1798G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.855 in 151,688 control chromosomes in the GnomAD database, including 55,616 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 0.85 (55616 hom., cov: 28)
• Consequence: MACC1-OT1 ENST00000435968.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286
• Publications: 6 publications found

Genes affected

MACC1-OT1 (HGNC:58196):

ENSG00000296332 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435968.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MACC1-OT1	NR_110114.1		n.111-1798G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MACC1-OT1	ENST00000415499.6	TSL:3	n.112-1798G>C		intron	N/A
	MACC1-OT1	ENST00000418442.1	TSL:3	n.240-1798G>C		intron	N/A
	MACC1-OT1	ENST00000435968.5	TSL:2	n.59-1798G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.855 AC: 129583 AN: 151568 Hom.: 55580 Cov.: 28

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.914

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.855 AC: 129676 AN: 151688 Hom.: 55616 Cov.: 28 AF XY: 0.851 AC XY: 63041 AN XY: 74094

African (AFR) AF: 0.855 AC: 35359 AN: 41344

American (AMR) AF: 0.864 AC: 13164 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 3196 AN: 3472

East Asian (EAS) AF: 0.605 AC: 3086 AN: 5102

South Asian (SAS) AF: 0.789 AC: 3797 AN: 4810

European-Finnish (FIN) AF: 0.839 AC: 8767 AN: 10454

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.875 AC: 59441 AN: 67970

Other (OTH) AF: 0.855 AC: 1795 AN: 2100

Alfa AF: 0.815 Hom.: 2507

Bravo AF: 0.855

Asia WGS AF: 0.706 AC: 2459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.21
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs6954796; hg19: chr7-20086982;