rs7270994

Variant names:

• chr20-4675170-G-A
• rs7270994
• ENST00000652447.1:n.87+9892C>T

Your query was ambiguous. Multiple possible variants found:

• chr20-4675170-G-A
• chr20-4675170-G-T

Variant summary

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

The ENST00000652447.1(ENSG00000293214):​n.87+9892C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,122 control chromosomes in the GnomAD database, including 2,973 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 0.17 (2973 hom., cov: 32)
• Consequence: ENSG00000293214 ENST00000652447.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 2 publications found

Genes affected

ENSG00000293214 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652447.1. 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
	ENSG00000293214	ENST00000652447.1		n.87+9892C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26286 AN: 152004 Hom.: 2967 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0341

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.173 AC: 26319 AN: 152122 Hom.: 2973 Cov.: 32 AF XY: 0.175 AC XY: 13034 AN XY: 74368

African (AFR) AF: 0.314 AC: 13028 AN: 41486

American (AMR) AF: 0.154 AC: 2352 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 377 AN: 3466

East Asian (EAS) AF: 0.0340 AC: 176 AN: 5176

South Asian (SAS) AF: 0.145 AC: 699 AN: 4828

European-Finnish (FIN) AF: 0.166 AC: 1755 AN: 10564

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7488 AN: 68000

Other (OTH) AF: 0.144 AC: 305 AN: 2114

Alfa AF: 0.125 Hom.: 745

Bravo AF: 0.177

Asia WGS AF: 0.105 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.1
DANN	Benign	0.70
PhyloP100		1.1

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: rs7270994;

hg19: chr20-4655816;