rs17578222

Variant names:

• chr7-51611603-C-A
• rs17578222
• ENST00000648455.1:n.352+41104C>A

Variant summary

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

The ENST00000648455.1(ENSG00000285741):​n.352+41104C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,118 control chromosomes in the GnomAD database, including 2,223 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 0.15 (2223 hom., cov: 32)
• Consequence: ENSG00000285741 ENST00000648455.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.998
• Publications: 1 publications found

Genes affected

ENSG00000285741 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648455.1. 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
	ENSG00000285741	ENST00000648455.1		n.352+41104C>A		intron	N/A
	ENSG00000285741	ENST00000769890.1		n.480+32134C>A		intron	N/A
	ENSG00000285741	ENST00000769891.1		n.469+32134C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23453 AN: 152000 Hom.: 2223 Cov.: 32

Gnomad AFR AF: 0.0574

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.154 AC: 23463 AN: 152118 Hom.: 2223 Cov.: 32 AF XY: 0.163 AC XY: 12116 AN XY: 74338

African (AFR) AF: 0.0573 AC: 2381 AN: 41528

American (AMR) AF: 0.190 AC: 2901 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 540 AN: 3470

East Asian (EAS) AF: 0.192 AC: 994 AN: 5170

South Asian (SAS) AF: 0.228 AC: 1098 AN: 4812

European-Finnish (FIN) AF: 0.304 AC: 3206 AN: 10548

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11886 AN: 68002

Other (OTH) AF: 0.158 AC: 333 AN: 2106

Alfa AF: 0.164 Hom.: 7604

Bravo AF: 0.137

Asia WGS AF: 0.178 AC: 615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.49
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs17578222; hg19: chr7-51679299;