rs3807050

Variant names:

• chr6-35545149-G-A
• rs3807050
• ENST00000450618.1:n.141-66G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-35545149-G-A
• chr6-35545149-G-C

Variant summary

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

The ENST00000450618.1(ENSG00000228559):​n.141-66G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,032 control chromosomes in the GnomAD database, including 2,958 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 0.18 (2953 hom., cov: 29)
  • Exomes 𝑓: 0.24 (5 hom.)
• Consequence: ENSG00000228559 ENST00000450618.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 2 publications found

Genes affected

ENSG00000228559 (HGNC:58100):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03135	NR_187689.1	n.182-66G>A		intron_variant	Intron 2 of 2
LINC03135	NR_187690.1	n.118-66G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228559	ENST00000450618.1	n.141-66G>A		intron_variant	Intron 2 of 2	5
ENSG00000228559	ENST00000658088.2	n.181-66G>A		intron_variant	Intron 2 of 2
ENSG00000228559	ENST00000664260.2	n.336-66G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27295 AN: 151800 Hom.: 2945 Cov.: 29

Gnomad AFR AF: 0.0783

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0983

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.150

GnomAD4 exome AF: 0.237 AC: 27 AN: 114 Hom.: 5 Cov.: 0 AF XY: 0.243 AC XY: 18 AN XY: 74

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 2 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.167 AC: 2 AN: 12

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4

European-Non Finnish (NFE) AF: 0.237 AC: 18 AN: 76

Other (OTH) AF: 0.357 AC: 5 AN: 14

GnomAD4 genome AF: 0.180 AC: 27327 AN: 151918 Hom.: 2953 Cov.: 29 AF XY: 0.181 AC XY: 13434 AN XY: 74212

African (AFR) AF: 0.0785 AC: 3256 AN: 41454

American (AMR) AF: 0.120 AC: 1833 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 645 AN: 3472

East Asian (EAS) AF: 0.0985 AC: 507 AN: 5148

South Asian (SAS) AF: 0.191 AC: 916 AN: 4806

European-Finnish (FIN) AF: 0.318 AC: 3342 AN: 10524

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16264 AN: 67930

Other (OTH) AF: 0.155 AC: 327 AN: 2108

Alfa AF: 0.120 Hom.: 245

Bravo AF: 0.159

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	13
DANN	Benign	0.93
PhyloP100		-0.30

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3807050; hg19: chr6-35512926;