rs7805622

Variant names:

• chr7-56483270-A-G
• rs7805622
• ENST00000436042.2:n.16T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-56483270-A-G
• chr7-56483270-A-T

Variant summary

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

The ENST00000436042.2(ENSG00000225488):​n.16T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.852 in 152,266 control chromosomes in the GnomAD database, including 55,701 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 0.85 (55666 hom., cov: 31)
  • Exomes 𝑓: 0.84 (35 hom.)
• Consequence: ENSG00000225488 ENST00000436042.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875
• Publications: 7 publications found

Genes affected

ENSG00000225488 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000436042.2. 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
	LOC100240728	NR_108095.1		n.50T>C		non_coding_transcript_exon	Exon 1 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225488	ENST00000436042.2	TSL:1	n.16T>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000225488	ENST00000651867.3		n.61T>C		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000225488	ENST00000665097.1		n.13T>C		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.852 AC: 129494 AN: 152050 Hom.: 55611 Cov.: 31

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.862

GnomAD4 exome AF: 0.837 AC: 82 AN: 98 Hom.: 35 Cov.: 0 AF XY: 0.803 AC XY: 53 AN XY: 66

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.667 AC: 20 AN: 30

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.911 AC: 51 AN: 56

Other (OTH) AF: 0.900 AC: 9 AN: 10

GnomAD4 genome AF: 0.852 AC: 129604 AN: 152168 Hom.: 55666 Cov.: 31 AF XY: 0.848 AC XY: 63097 AN XY: 74386

African (AFR) AF: 0.949 AC: 39428 AN: 41548

American (AMR) AF: 0.888 AC: 13588 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.864 AC: 2999 AN: 3472

East Asian (EAS) AF: 0.606 AC: 3117 AN: 5140

South Asian (SAS) AF: 0.887 AC: 4279 AN: 4824

European-Finnish (FIN) AF: 0.716 AC: 7568 AN: 10570

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.819 AC: 55711 AN: 68000

Other (OTH) AF: 0.862 AC: 1822 AN: 2114

Alfa AF: 0.836 Hom.: 155052

Bravo AF: 0.865

Asia WGS AF: 0.783 AC: 2722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.1
DANN	Benign	0.20
PhyloP100		-0.88

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: rs7805622;

hg19: chr7-56550963;