1-72548334-G-C

Position:

• chr1-72548334-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653965.1(ENSG00000286863):​n.397-6877G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.946 in 151,932 control chromosomes in the GnomAD database, including 68,216 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 (68216 hom., cov: 32)
• Consequence: ENSG00000286863 ENST00000653965.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

Genes affected

ENSG00000286863 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378797	XR_001737670.2	n.651-6877G>C		intron_variant
LOC105378797	XR_001737671.3	n.521-9527G>C		intron_variant
LOC105378797	XR_947505.3	n.521-6877G>C		intron_variant
LOC105378797	XR_947506.3	n.473-6877G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286863	ENST00000653965.1	n.397-6877G>C		intron_variant
ENSG00000286863	ENST00000662505.1	n.49-6877G>C		intron_variant
ENSG00000286863	ENST00000665984.1	n.202-6877G>C		intron_variant
ENSG00000286863	ENST00000688733.1	n.217-6877G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.946 AC: 143581 AN: 151814 Hom.: 68169 Cov.: 32

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.946

Gnomad ASJ AF: 0.992

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.991

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.960

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

GnomAD4 genome AF: 0.946 AC: 143685 AN: 151932 Hom.: 68216 Cov.: 32 AF XY: 0.948 AC XY: 70389 AN XY: 74278

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.946

Gnomad4 ASJ AF: 0.992

Gnomad4 EAS AF: 0.951

Gnomad4 SAS AF: 0.991

Gnomad4 FIN AF: 0.995

Gnomad4 NFE AF: 0.986

Gnomad4 OTH AF: 0.960

Alfa AF: 0.962 Hom.: 8216

Bravo AF: 0.939

Asia WGS AF: 0.973 AC: 3381 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1418624; hg19: chr1-73014017;