chr7-50200973-A-G

Variant names:

• chr7-50200973-A-G
• rs1598702
• ENST00000781401.1:n.144+3046A>G

Variant summary

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

The ENST00000781401.1(ENSG00000301758):​n.144+3046A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,132 control chromosomes in the GnomAD database, including 44,577 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 0.76 (44577 hom., cov: 32)
• Consequence: ENSG00000301758 ENST00000781401.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518
• Publications: 0 publications found

Genes affected

ENSG00000301758 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000781401.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301758	ENST00000781401.1		n.144+3046A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115603 AN: 152012 Hom.: 44529 Cov.: 32

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.761 AC: 115716 AN: 152132 Hom.: 44577 Cov.: 32 AF XY: 0.761 AC XY: 56599 AN XY: 74392

African (AFR) AF: 0.780 AC: 32346 AN: 41494

American (AMR) AF: 0.805 AC: 12297 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2205 AN: 3468

East Asian (EAS) AF: 0.381 AC: 1965 AN: 5164

South Asian (SAS) AF: 0.774 AC: 3725 AN: 4814

European-Finnish (FIN) AF: 0.832 AC: 8823 AN: 10600

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.764 AC: 51976 AN: 67992

Other (OTH) AF: 0.737 AC: 1556 AN: 2110

Alfa AF: 0.772 Hom.: 5662

Bravo AF: 0.753

Asia WGS AF: 0.676 AC: 2355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.2
DANN	Benign	0.70
PhyloP100		-0.52

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1598702;

hg19: chr7-50240569;