rs6774280

Variant names:

• chr3-6214310-T-C
• rs6774280
• ENST00000425894.2:n.1404-600T>C

Variant summary

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

The ENST00000425894.2(ENSG00000229642):​n.1404-600T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 150,590 control chromosomes in the GnomAD database, including 2,817 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 0.19 (2817 hom., cov: 31)
• Consequence: ENSG00000229642 ENST00000425894.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238
• Publications: 6 publications found

Genes affected

ENSG00000229642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425894.2. 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
	ENSG00000229642	ENST00000425894.2	TSL:3	n.1404-600T>C		intron	N/A
	ENSG00000226022	ENST00000435651.2	TSL:3	n.95+65732T>C		intron	N/A
	ENSG00000229642	ENST00000779001.1		n.1356-600T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28513 AN: 150502 Hom.: 2816 Cov.: 31

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0574

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.122

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.189 AC: 28522 AN: 150590 Hom.: 2817 Cov.: 31 AF XY: 0.187 AC XY: 13759 AN XY: 73394

African (AFR) AF: 0.170 AC: 6988 AN: 40992

American (AMR) AF: 0.241 AC: 3629 AN: 15042

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 780 AN: 3466

East Asian (EAS) AF: 0.0570 AC: 294 AN: 5158

South Asian (SAS) AF: 0.179 AC: 857 AN: 4784

European-Finnish (FIN) AF: 0.178 AC: 1795 AN: 10058

Middle Eastern (MID) AF: 0.131 AC: 38 AN: 290

European-Non Finnish (NFE) AF: 0.201 AC: 13609 AN: 67798

Other (OTH) AF: 0.177 AC: 371 AN: 2094

Alfa AF: 0.199 Hom.: 7953

Bravo AF: 0.194

Asia WGS AF: 0.117 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	7.6
DANN	Benign	0.18
PhyloP100		0.24

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: rs6774280;

hg19: chr3-6255997;