rs7220740

Variant names:

• chr17-61663432-C-A
• rs7220740
• ENST00000849359.1:n.173-83C>A

Your query was ambiguous. Multiple possible variants found:

• chr17-61663432-C-A
• chr17-61663432-C-G
• chr17-61663432-C-T

Variant summary

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

The ENST00000849359.1(ENSG00000310374):​n.173-83C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 151,982 control chromosomes in the GnomAD database, including 6,689 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 0.29 (6689 hom., cov: 32)
• Consequence: ENSG00000310374 ENST00000849359.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.665
• Publications: 5 publications found

Genes affected

ENSG00000310374 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849359.1. 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
	ENSG00000310374	ENST00000849359.1		n.173-83C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44370 AN: 151864 Hom.: 6680 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.292 AC: 44409 AN: 151982 Hom.: 6689 Cov.: 32 AF XY: 0.290 AC XY: 21574 AN XY: 74302

African (AFR) AF: 0.281 AC: 11662 AN: 41446

American (AMR) AF: 0.303 AC: 4615 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 818 AN: 3468

East Asian (EAS) AF: 0.497 AC: 2567 AN: 5168

South Asian (SAS) AF: 0.230 AC: 1105 AN: 4812

European-Finnish (FIN) AF: 0.224 AC: 2366 AN: 10566

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20310 AN: 67948

Other (OTH) AF: 0.301 AC: 636 AN: 2112

Alfa AF: 0.270 Hom.: 3628

Bravo AF: 0.297

Asia WGS AF: 0.320 AC: 1111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.62
DANN	Benign	0.61
PhyloP100		-0.67

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: rs7220740;

hg19: chr17-59740793;