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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901293	XR_007059536.1	n.204-84T>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297504	ENST00000748463.1	n.481T>A		non_coding_transcript_exon_variant	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 v4.3

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

Other links and lift over

dbSNP: rs3800307; hg19: chr6-27185792;