3-53066198-G-T

Variant names:

• chr3-53066198-G-T
• rs6770152
• ENST00000607283.5:n.*93+11490C>A

Variant summary

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

The ENST00000607283.5(ENSG00000272305):​n.*93+11490C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,078 control chromosomes in the GnomAD database, including 28,553 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 0.61 (28553 hom., cov: 32)
• Consequence: ENSG00000272305 ENST00000607283.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.963
• Publications: 43 publications found

Genes affected

ENSG00000272305 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607283.5. 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
	ENSG00000272305	ENST00000607283.5	TSL:5	n.*93+11490C>A		intron	N/A	ENSP00000475819.1	U3KQE9
	ENSG00000272305	ENST00000607203.1	TSL:5	n.*240+11490C>A		intron	N/A	ENSP00000475866.1	U3KQG8
	ENSG00000272305	ENST00000607495.5	TSL:5	n.*346+11490C>A		intron	N/A	ENSP00000475958.1	U3KQK6

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92428 AN: 151960 Hom.: 28522 Cov.: 32

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.608 AC: 92509 AN: 152078 Hom.: 28553 Cov.: 32 AF XY: 0.608 AC XY: 45235 AN XY: 74356

African (AFR) AF: 0.689 AC: 28580 AN: 41462

American (AMR) AF: 0.606 AC: 9259 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1955 AN: 3472

East Asian (EAS) AF: 0.390 AC: 2016 AN: 5168

South Asian (SAS) AF: 0.536 AC: 2587 AN: 4826

European-Finnish (FIN) AF: 0.614 AC: 6492 AN: 10580

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.584 AC: 39704 AN: 67968

Other (OTH) AF: 0.576 AC: 1217 AN: 2112

Alfa AF: 0.595 Hom.: 47183

Bravo AF: 0.608

Asia WGS AF: 0.481 AC: 1673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.077
DANN	Benign	0.32
PhyloP100		-0.96

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: rs6770152;

hg19: chr3-53100214;