rs3800307

Variant names:

• chr6-27218013-T-A
• rs3800307
• ENST00000748463.1:n.481T>A

Variant summary

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

The ENST00000748463.1(ENSG00000297504):​n.481T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 151,776 control chromosomes in the GnomAD database, including 2,103 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 0.16 (2103 hom., cov: 31)
• Consequence: ENSG00000297504 ENST00000748463.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335
• Publications: 28 publications found

Genes affected

ENSG00000297504 (HGNC:):

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 = 0.194 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000748463.1. 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
	ENSG00000297504	ENST00000748463.1		n.481T>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24101 AN: 151658 Hom.: 2103 Cov.: 31

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0190

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.159 AC: 24102 AN: 151776 Hom.: 2103 Cov.: 31 AF XY: 0.152 AC XY: 11245 AN XY: 74148

African (AFR) AF: 0.144 AC: 5964 AN: 41362

American (AMR) AF: 0.134 AC: 2050 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 388 AN: 3466

East Asian (EAS) AF: 0.0188 AC: 97 AN: 5158

South Asian (SAS) AF: 0.112 AC: 539 AN: 4798

European-Finnish (FIN) AF: 0.105 AC: 1101 AN: 10528

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.197 AC: 13347 AN: 67910

Other (OTH) AF: 0.149 AC: 315 AN: 2108

Alfa AF: 0.175 Hom.: 306

Bravo AF: 0.161

Asia WGS AF: 0.0750 AC: 262 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	1.5
DANN	Benign	0.60
PhyloP100		-0.34

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: rs3800307;

hg19: chr6-27185792;