1-247628464-C-T

Variant names:

• chr1-247628464-C-T
• rs1306161
• ENST00000435333.6:n.294+7391G>A

Variant summary

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

The ENST00000435333.6(ENSG00000236817):​n.294+7391G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.954 in 152,212 control chromosomes in the GnomAD database, including 69,558 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 0.95 (69558 hom., cov: 31)
• Consequence: ENSG00000236817 ENST00000435333.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 0 publications found

Genes affected

ENSG00000236817 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.987 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724446	NR_188589.1	n.225+7391G>A		intron_variant	Intron 2 of 2
LOC102724446	NR_188590.1	n.437+7391G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000236817	ENST00000435333.6	n.294+7391G>A		intron_variant	Intron 2 of 2	3
ENSG00000236817	ENST00000446347.1	n.437+7391G>A		intron_variant	Intron 2 of 2	2
ENSG00000236817	ENST00000746874.1	n.221+7391G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.955 AC: 145177 AN: 152094 Hom.: 69512 Cov.: 31

Gnomad AFR AF: 0.872

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.974

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.993

Gnomad OTH AF: 0.960

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

GnomAD4 genome AF: 0.954 AC: 145278 AN: 152212 Hom.: 69558 Cov.: 31 AF XY: 0.955 AC XY: 71040 AN XY: 74426

African (AFR) AF: 0.872 AC: 36190 AN: 41496

American (AMR) AF: 0.974 AC: 14900 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3293 AN: 3472

East Asian (EAS) AF: 0.986 AC: 5085 AN: 5156

South Asian (SAS) AF: 0.944 AC: 4555 AN: 4826

European-Finnish (FIN) AF: 0.985 AC: 10463 AN: 10622

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.993 AC: 67577 AN: 68022

Other (OTH) AF: 0.960 AC: 2030 AN: 2114

Alfa AF: 0.967 Hom.: 17913

Bravo AF: 0.951

Asia WGS AF: 0.961 AC: 3343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.77
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1306161; hg19: chr1-247791766;