1-203295900-T-A

Variant names:

• chr1-203295900-T-A
• rs6663606
• ENST00000432511.4:n.779-3403A>T

Variant summary

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

The ENST00000432511.4(BTG2-DT):​n.779-3403A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 151,822 control chromosomes in the GnomAD database, including 14,247 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 0.40 (14247 hom., cov: 30)
• Consequence: BTG2-DT ENST00000432511.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 3 publications found

Genes affected

BTG2-DT (HGNC:49452): (BTG2 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000432511.4. 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
	BTG2-DT	ENST00000432511.4	TSL:3	n.779-3403A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.402 AC: 60934 AN: 151704 Hom.: 14239 Cov.: 30

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.401 AC: 60946 AN: 151822 Hom.: 14247 Cov.: 30 AF XY: 0.405 AC XY: 30006 AN XY: 74156

African (AFR) AF: 0.182 AC: 7532 AN: 41396

American (AMR) AF: 0.365 AC: 5567 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1721 AN: 3464

East Asian (EAS) AF: 0.188 AC: 965 AN: 5142

South Asian (SAS) AF: 0.357 AC: 1720 AN: 4818

European-Finnish (FIN) AF: 0.633 AC: 6652 AN: 10508

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35213 AN: 67914

Other (OTH) AF: 0.439 AC: 927 AN: 2112

Alfa AF: 0.459 Hom.: 2169

Bravo AF: 0.372

Asia WGS AF: 0.303 AC: 1056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.064
DANN	Benign	0.59
PhyloP100		-2.0

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: rs6663606;

hg19: chr1-203265028;