rs7121790

Positions:

• chr11-45043414-G-A
• chr11-45043414-G-C

Variant summary

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

The ENST00000654627.1(ENSG00000287984):​n.500-281G>A 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 0.153 in 152,238 control chromosomes in the GnomAD database, including 2,370 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 0.15 (2370 hom., cov: 33)
• Consequence: ENST00000654627.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.839

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376650	XR_931237.3	n.691-281G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654627.1	n.500-281G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23287 AN: 152120 Hom.: 2372 Cov.: 33

Gnomad AFR AF: 0.0438

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0841

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.153 AC: 23274 AN: 152238 Hom.: 2370 Cov.: 33 AF XY: 0.149 AC XY: 11114 AN XY: 74432

Gnomad4 AFR AF: 0.0437

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0838

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.161

Alfa AF: 0.207 Hom.: 6949

Bravo AF: 0.144

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.3
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7121790; hg19: chr11-45064965;