rs7722135

Variant names:

• chr5-86998852-C-T
• rs7722135
• ENST00000503349.1:n.219+31313C>T

Variant summary

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

The ENST00000503349.1(ENSG00000249061):​n.219+31313C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,086 control chromosomes in the GnomAD database, including 4,693 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 0.24 (4693 hom., cov: 32)
• Consequence: ENSG00000249061 ENST00000503349.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• Publications: 7 publications found

Genes affected

ENSG00000249061 (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 (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503349.1. 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
	ENSG00000249061	ENST00000503349.1	TSL:2	n.219+31313C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36683 AN: 151968 Hom.: 4687 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.0368

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.241 AC: 36720 AN: 152086 Hom.: 4693 Cov.: 32 AF XY: 0.243 AC XY: 18076 AN XY: 74340

African (AFR) AF: 0.278 AC: 11516 AN: 41488

American (AMR) AF: 0.202 AC: 3081 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3470

East Asian (EAS) AF: 0.0365 AC: 189 AN: 5178

South Asian (SAS) AF: 0.175 AC: 844 AN: 4816

European-Finnish (FIN) AF: 0.317 AC: 3350 AN: 10576

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.235 AC: 16001 AN: 67980

Other (OTH) AF: 0.234 AC: 493 AN: 2110

Alfa AF: 0.244 Hom.: 809

Bravo AF: 0.231

Asia WGS AF: 0.115 AC: 403 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.42
PhyloP100		0.042

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: rs7722135;

hg19: chr5-86294669;