rs2703175

Positions:

• chr18-41469123-A-G
• chr18-41469123-A-T

Variant summary

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

The ENST00000670702.1(ENSG00000286328):​n.200-35011A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.888 in 152,242 control chromosomes in the GnomAD database, including 60,083 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 0.89 (60083 hom., cov: 32)
• Consequence: ENST00000670702.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454

Genes affected

(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 (AFR) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000670702.1	n.200-35011A>G		intron_variant, non_coding_transcript_variant
KC6	ENST00000600644.2	n.314-1343T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.888 AC: 135040 AN: 152124 Hom.: 60036 Cov.: 32

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.925

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.888 AC: 135147 AN: 152242 Hom.: 60083 Cov.: 32 AF XY: 0.884 AC XY: 65817 AN XY: 74424

Gnomad4 AFR AF: 0.919

Gnomad4 AMR AF: 0.844

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.801

Gnomad4 FIN AF: 0.880

Gnomad4 NFE AF: 0.890

Gnomad4 OTH AF: 0.895

Alfa AF: 0.889 Hom.: 59606

Bravo AF: 0.886

Asia WGS AF: 0.847 AC: 2943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.83
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2703175; hg19: chr18-39049087;